Variant report

Variant	rs3195954
Chromosome Location	chr1:114354654-114354655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:335)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:335 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr1:114354521-114355426	SK-N-SH	brain:	n/a	n/a
2	CCNT2	chr1:114354208-114355391	K562	blood:	n/a	n/a
3	YY1	chr1:114354373-114355458	ECC-1	luminal epithelium:	n/a	chr1:114354579-114354599
4	KAP1	chr1:114354636-114355474	U2OS	brain:	n/a	n/a
5	ZMIZ1	chr1:114354486-114355462	K562	blood:	n/a	n/a
6	MAX	chr1:114354296-114355555	SK-N-SH	brain:	n/a	n/a
7	GABPA	chr1:114353816-114356357	MCF-7	breast:	n/a	n/a
8	SIN3A	chr1:114353875-114355647	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr1:114354427-114355682	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:114354463-114355035	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr1:114353902-114355669	Hela-S3	cervix:	n/a	n/a
12	REST	chr1:114353810-114355766	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr1:114354415-114355641	GM10847	blood:	n/a	n/a
14	TCF3	chr1:114354617-114354937	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:114354143-114355675	MCF-7	breast:	n/a	n/a
16	POLR2A	chr1:114354051-114355558	GM12878	blood:	n/a	n/a
17	CHD2	chr1:114354038-114355445	Hela-S3	cervix:	n/a	n/a
18	TAF1	chr1:114354491-114355100	GM12891	blood:	n/a	n/a
19	RFX5	chr1:114353926-114355471	Hela-S3	cervix:	n/a	n/a
20	TAF1	chr1:114353750-114355475	K562	blood:	n/a	n/a
21	POLR2A	chr1:114354505-114355679	GM12878	blood:	n/a	n/a
22	SP1	chr1:114354606-114355413	A549	lung:	n/a	chr1:114354988-114354999
23	CREB1	chr1:114354313-114355481	HepG2	liver:	n/a	n/a
24	MAX	chr1:114353591-114355868	MCF-7	breast:	n/a	n/a
25	POLR2A	chr1:114354212-114355464	HL-60	blood:	n/a	n/a
26	TCF12	chr1:114353866-114355830	MCF-7	breast:	n/a	n/a
27	MXI1	chr1:114353706-114355698	IMR90	lung:	n/a	n/a
28	TBP	chr1:114354642-114355488	HepG2	liver:	n/a	n/a
29	KAP1	chr1:114354214-114355523	HEK293	kidney:	n/a	n/a
30	CEBPB	chr1:114354566-114355536	H1-hESC	embryonic stem cell:	n/a	n/a
31	BCLAF1	chr1:114354500-114355422	GM12878	blood:	n/a	n/a
32	HCFC1	chr1:114354307-114355746	K562	blood:	n/a	n/a
33	POLR2A	chr1:114354300-114355639	HUVEC	blood vessel:	n/a	n/a
34	E2F6	chr1:114354424-114354741	K562	blood:	n/a	n/a
35	POLR2A	chr1:114353972-114355763	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:114354195-114355609	HCT-116	colon:	n/a	n/a
37	MAZ	chr1:114354147-114355695	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:114354145-114355710	MCF-7	breast:	n/a	n/a
39	POLR2A	chr1:114353923-114355486	HepG2	liver:	n/a	n/a
40	TAF1	chr1:114354215-114355475	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr1:114354295-114355596	HL-60	blood:	n/a	n/a
42	PAX5	chr1:114354575-114355483	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:114354389-114355728	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr1:114354579-114355577	PFSK-1	brain:	n/a	n/a
45	YY1	chr1:114354072-114355499	SK-N-SH	brain:	n/a	chr1:114354579-114354599
46	MAFK	chr1:114354626-114355713	K562	blood:	n/a	n/a
47	MXI1	chr1:114353147-114355793	SK-N-SH	brain:	n/a	n/a
48	EGR1	chr1:114353034-114356186	MCF-7	breast:	n/a	n/a
49	TRIM28	chr1:114354609-114355765	K562	blood:	n/a	n/a
50	POLR2A	chr1:114354311-114355553	K562	blood:	n/a	n/a

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114353442..114355343-chr17:57922180..57925150,2	MCF-7	breast:
2	chr1:114353355..114355590-chr17:57860876..57862433,2	MCF-7	breast:
3	chr1:114324677..114327047-chr1:114352445..114354886,5	MCF-7	breast:
4	chr1:114354384..114355228-chr20:42085712..42086698,2	HCT-116	colon:
5	chr1:114351776..114354778-chr1:114417690..114420488,3	MCF-7	breast:
6	chr1:114353911..114356847-chr1:114364689..114367754,3	K562	blood:
7	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:
8	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
9	chr1:114352914..114355173-chr8:67972851..67974547,2	MCF-7	breast:
10	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
11	chr1:114353271..114354789-chr1:114442800..114445051,2	MCF-7	breast:
12	chr1:114353393..114356662-chr20:49346921..49350434,3	MCF-7	breast:
13	chr1:114354399..114356647-chr1:115051838..115054168,3	MCF-7	breast:
14	chr1:114354416..114355376-chr2:70520378..70521068,2	Hela-S3	cervix:
15	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
16	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:
17	chr1:114354554..114355120-chr17:58603243..58604087,2	MCF-7	breast:
18	chr1:114354097..114356743-chr1:115299184..115300784,2	MCF-7	breast:
19	chr1:108226178..108228590-chr1:114353094..114356101,3	MCF-7	breast:
20	chr1:114353074..114355128-chr9:133814434..133817147,2	MCF-7	breast:
21	chr1:114307008..114312126-chr1:114352475..114355930,7	MCF-7	breast:
22	chr1:114308167..114310817-chr1:114354142..114357057,3	K562	blood:
23	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
24	chr1:108229330..108231475-chr1:114352461..114355425,3	MCF-7	breast:
25	chr1:114353249..114355008-chr17:59488182..59490622,2	MCF-7	breast:
26	chr1:114279918..114281737-chr1:114354339..114355849,2	MCF-7	breast:
27	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
28	chr1:114353164..114356409-chr1:114439569..114442509,4	MCF-7	breast:
29	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
30	chr1:114352766..114354968-chr1:114504894..114507135,2	MCF-7	breast:
31	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
32	chr1:114353223..114356831-chr1:115298921..115302043,5	MCF-7	breast:
33	chr1:114352743..114357488-chr1:114365626..114369516,6	MCF-7	breast:
34	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
35	chr1:114353109..114354990-chr1:114522325..114525289,2	MCF-7	breast:
36	chr1:108291627..108293246-chr1:114353081..114355950,2	MCF-7	breast:
37	chr1:114299507..114303267-chr1:114354438..114356409,4	K562	blood:
38	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
39	chr1:114352670..114354884-chr1:114372315..114375244,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231128	TF binding region
ENSG00000267637	Chromatin interaction
ENSG00000143977	Chromatin interaction
ENSG00000226167	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000130720	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000134215	Chromatin interaction
ENSG00000121022	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000116774	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11582409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584821	0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17031795	0.86[ASN][1000 genomes]
rs17274627	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs17359281	0.88[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs17463292	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17464525	0.85[GIH][hapmap]
rs17509844	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17510162	0.82[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34122108	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35173468	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761935	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789604	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789608	0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4393155	0.88[ASN][1000 genomes]
rs4589108	0.86[ASN][1000 genomes]
rs4839000	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[ASN][1000 genomes]
rs4839331	0.88[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4839333	0.88[CHB][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs4839341	0.86[ASN][1000 genomes]
rs4839346	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55646484	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55940960	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55951516	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658523	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3195954	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs3195954	CD53	cis	parietal	SCAN
rs3195954	PHTF1	cis	lymphoblastoid	seeQTL
rs3195954	RHOC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114351800-114355400	Active TSS	NHLF	lung
2	chr1:114351800-114355600	Active TSS	Psoas Muscle	Psoas
3	chr1:114352000-114355800	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr1:114352000-114355800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:114352200-114355400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:114352200-114355400	Active TSS	GM12878-XiMat	blood
7	chr1:114352200-114355400	Active TSS	Hela-S3	cervix
8	chr1:114352200-114355800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:114352400-114355200	Active TSS	Primary T cells fromperipheralblood	blood
10	chr1:114352400-114355400	Active TSS	Fetal Intestine Large	intestine
11	chr1:114352400-114355400	Active TSS	Fetal Thymus	thymus
12	chr1:114352400-114355800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:114352400-114356200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:114352600-114355400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:114352600-114355400	Active TSS	HSMM	muscle
16	chr1:114352600-114355600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:114352600-114355600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:114352600-114355800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:114352600-114355800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:114352600-114355800	Active TSS	A549	lung
21	chr1:114352600-114355800	Active TSS	HSMMtube	muscle
22	chr1:114352800-114355400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:114352800-114355400	Active TSS	Colonic Mucosa	Colon
24	chr1:114352800-114355400	Active TSS	Fetal Intestine Small	intestine
25	chr1:114352800-114355400	Active TSS	K562	blood
26	chr1:114352800-114355600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:114352800-114355600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:114352800-114355600	Active TSS	Aorta	Aorta
29	chr1:114352800-114355600	Active TSS	Left Ventricle	heart
30	chr1:114352800-114355600	Active TSS	Ovary	ovary
31	chr1:114352800-114355600	Active TSS	Rectal Smooth Muscle	rectum
32	chr1:114352800-114355600	Active TSS	Right Ventricle	heart
33	chr1:114352800-114355600	Active TSS	NHDF-Ad	bronchial
34	chr1:114352800-114355800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr1:114352800-114355800	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr1:114352800-114355800	Active TSS	Fetal Kidney	kidney
37	chr1:114353000-114355000	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr1:114353000-114355400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:114353000-114355400	Active TSS	Fetal Stomach	stomach
40	chr1:114353000-114355400	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr1:114353000-114355400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:114353000-114355800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr1:114353000-114356000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:114353200-114355400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:114353200-114355400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:114353200-114355400	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:114353200-114355400	Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:114353200-114355400	Active TSS	Colon Smooth Muscle	Colon
49	chr1:114353200-114355400	Active TSS	Duodenum Mucosa	Duodenum
50	chr1:114353200-114355400	Active TSS	HMEC	breast

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