Variant report

Variant	rs3795474
Chromosome Location	chr1:246729990-246729991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr1:246729042-246730105	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:246729066-246730487	K562	blood:	n/a	n/a
3	SP2	chr1:246729180-246730227	H1-hESC	embryonic stem cell:	n/a	n/a
4	GABPA	chr1:246729070-246730069	A549	lung:	n/a	chr1:246729612-246729619 chr1:246729570-246729579 chr1:246729570-246729581 chr1:246729547-246729554 chr1:246729567-246729581
5	ELF1	chr1:246729149-246730121	GM12878	blood:	n/a	chr1:246729615-246729624 chr1:246729547-246729556 chr1:246729544-246729557 chr1:246729610-246729619
6	SIN3AK20	chr1:246729073-246730429	A549	lung:	n/a	n/a
7	POLR2A	chr1:246729137-246730118	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr1:246729152-246730012	HL-60	blood:	n/a	chr1:246729726-246729733 chr1:246729610-246729619 chr1:246729547-246729556 chr1:246729545-246729558 chr1:246729608-246729621
9	POLR2A	chr1:246729259-246730225	A549	lung:	n/a	n/a
10	MYC	chr1:246728734-246730845	K562	blood:	n/a	chr1:246730385-246730392
11	POLR2A	chr1:246729172-246730442	HL-60	blood:	n/a	n/a
12	GATA3	chr1:246729172-246730192	A549	lung:	n/a	n/a
13	GABPA	chr1:246728844-246730291	A549	lung:	n/a	chr1:246729612-246729619 chr1:246729570-246729579 chr1:246729570-246729581 chr1:246729547-246729554 chr1:246729567-246729581
14	BHLHE40	chr1:246729128-246730340	K562	blood:	n/a	n/a
15	ZKSCAN1	chr1:246729332-246730112	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:246729094-246731210	GM12891	blood:	n/a	n/a
17	TAF7	chr1:246729186-246730234	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZC3H11A	chr1:246729376-246730593	K562	blood:	n/a	n/a
19	JUND	chr1:246729302-246730407	A549	lung:	n/a	n/a
20	RCOR1	chr1:246729172-246730515	K562	blood:	n/a	n/a
21	RCOR1	chr1:246729350-246730887	Hela-S3	cervix:	n/a	n/a
22	ZMIZ1	chr1:246729244-246730404	K562	blood:	n/a	n/a
23	HEY1	chr1:246729255-246730373	K562	blood:	n/a	n/a
24	MAX	chr1:246729228-246730081	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr1:246729142-246730471	A549	lung:	n/a	chr1:246730385-246730392
26	MAX	chr1:246729023-246730981	ECC-1	luminal epithelium:	n/a	chr1:246730385-246730392
27	CHD2	chr1:246729348-246730202	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr1:246729172-246730330	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAL1	chr1:246729401-246730323	K562	blood:	n/a	n/a
30	TEAD4	chr1:246729003-246731470	K562	blood:	n/a	chr1:246730585-246730594
31	POLR2A	chr1:246729268-246730024	U87	brain:	n/a	n/a
32	POLR2A	chr1:246729176-246730438	K562	blood:	n/a	n/a
33	SP2	chr1:246729261-246730171	HepG2	liver:	n/a	n/a
34	EP300	chr1:246729298-246730017	K562	blood:	n/a	chr1:246729606-246729620
35	MAX	chr1:246729099-246730501	MCF-7	breast:	n/a	chr1:246730385-246730392
36	CREB1	chr1:246728988-246730332	HepG2	liver:	n/a	n/a
37	SMC3	chr1:246729300-246730422	GM12878	blood:	n/a	chr1:246730239-246730249
38	YY1	chr1:246729371-246730284	GM12878	blood:	n/a	n/a
39	SP1	chr1:246729366-246730020	H1-hESC	embryonic stem cell:	n/a	n/a
40	FOXM1	chr1:246729145-246730026	GM12878	blood:	n/a	n/a
41	YY1	chr1:246729485-246730420	K562	blood:	n/a	n/a
42	RFX5	chr1:246729126-246731037	Hela-S3	cervix:	n/a	chr1:246730776-246730785
43	POLR2A	chr1:246729223-246730032	HUVEC	blood vessel:	n/a	n/a
44	KAP1	chr1:246729525-246730052	U2OS	brain:	n/a	n/a
45	EBF1	chr1:246729393-246730370	GM12878	blood:	n/a	chr1:246730204-246730213 chr1:246730203-246730214
46	MYC	chr1:246729118-246730403	NB4	blood:	n/a	chr1:246730385-246730392
47	TAF1	chr1:246729231-246730198	HepG2	liver:	n/a	n/a
48	GTF2B	chr1:246729369-246730373	K562	blood:	n/a	n/a
49	POLR2A	chr1:246729308-246730382	HCT-116	colon:	n/a	n/a
50	MAX	chr1:246728967-246730080	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:246685591..246688881-chr1:246727054..246730014,3	K562	blood:
2	chr1:19638692..19639192-chr1:246729163..246730124,2	Hela-S3	cervix:
3	chr1:246729874..246731842-chr1:246862649..246864902,2	K562	blood:
4	chr1:246729197..246730166-chr14:75745608..75746363,2	Hela-S3	cervix:
5	chr1:246729967..246732161-chr22:19156837..19159425,2	K562	blood:

Variant related genes	Relation type
TFB2M	TF binding region
ENSG00000242042	Chromatin interaction
ENSG00000260924	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000040487	Chromatin interaction
ENSG00000227728	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12742513	0.80[ASN][1000 genomes]
rs12744338	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12746341	0.84[ASN][1000 genomes]
rs12748061	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12750641	0.95[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7536768	0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7547043	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1005573	chr1:246378676-246740427	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv535405	chr1:246378676-246740427	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2757779	chr1:246407146-246740944	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	esv2759012	chr1:246407146-246740944	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv428346	chr1:246407146-246740944	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
19	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
24	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
25	nsv522963	chr1:246696596-246747586	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv527464	chr1:246698653-246742157	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	nsv873420	chr1:246706139-246755124	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
28	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
29	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
30	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
31	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246727600-246730800	Active TSS	Ovary	ovary
2	chr1:246727600-246731400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:246727800-246731000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:246727800-246731200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:246727800-246731200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:246727800-246731200	Active TSS	Osteobl	bone
7	chr1:246727800-246731400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:246727800-246732000	Active TSS	NHLF	lung
9	chr1:246728000-246730400	Active TSS	Pancreas	Pancrea
10	chr1:246728000-246730800	Active TSS	HMEC	breast
11	chr1:246728000-246731000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:246728000-246731000	Active TSS	A549	lung
13	chr1:246728000-246731400	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:246728000-246732600	Active TSS	K562	blood
15	chr1:246728200-246731000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:246728200-246731000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:246728200-246731000	Active TSS	Fetal Kidney	kidney
18	chr1:246728200-246731200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:246728200-246731200	Active TSS	NHDF-Ad	bronchial
20	chr1:246728200-246731400	Active TSS	Psoas Muscle	Psoas
21	chr1:246728200-246731400	Active TSS	Right Atrium	heart
22	chr1:246728400-246730400	Active TSS	Rectal Smooth Muscle	rectum
23	chr1:246728400-246731000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr1:246728400-246731000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:246728400-246731200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:246728400-246731200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:246728400-246731200	Active TSS	Right Ventricle	heart
28	chr1:246728400-246731400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:246728400-246731400	Active TSS	Aorta	Aorta
30	chr1:246728600-246730400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:246728600-246730400	Active TSS	Gastric	stomach
32	chr1:246728600-246730600	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:246728600-246730800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:246728600-246730800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:246728600-246730800	Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:246728600-246730800	Active TSS	Stomach Smooth Muscle	stomach
37	chr1:246728600-246730800	Bivalent/Poised TSS	HepG2	liver
38	chr1:246728600-246730800	Active TSS	NH-A	brain
39	chr1:246728600-246731000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:246728600-246731000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:246728600-246731000	Active TSS	HSMM	muscle
42	chr1:246728600-246731000	Active TSS	HSMMtube	muscle
43	chr1:246728600-246731200	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:246728600-246731200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr1:246728600-246731200	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr1:246728600-246731200	Active TSS	GM12878-XiMat	blood
47	chr1:246728600-246731400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:246728600-246731400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:246728600-246731400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:246728800-246730000	Active TSS	Duodenum Smooth Muscle	Duodenum

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