Variant report

Variant	rs7535258
Chromosome Location	chr1:147013005-147013006
allele	A/G
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	TAF7	chr1:147012752-147013693	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr1:147012556-147013064	H1-hESC	embryonic stem cell:	n/a	chr1:147012761-147012771 chr1:147012760-147012772
3	SP1	chr1:147012988-147013517	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr1:147012613-147013570	ECC-1	luminal epithelium:	n/a	n/a
5	NFIC	chr1:147012666-147013589	ECC-1	luminal epithelium:	n/a	n/a
6	TEAD4	chr1:147012814-147013365	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:147012644-147013668	U87	brain:	n/a	n/a
8	RAD21	chr1:147012571-147013327	SK-N-SH_RA	brain:	n/a	n/a
9	MAX	chr1:147012632-147013426	SK-N-SH	brain:	n/a	n/a
10	SIN3AK20	chr1:147012750-147013021	SK-N-SH	brain:	n/a	n/a
11	SP1	chr1:147012675-147013855	H1-hESC	embryonic stem cell:	n/a	chr1:147012821-147012830
12	TCF12	chr1:147012589-147013540	A549	lung:	n/a	n/a
13	ZZZ3	chr1:147012707-147013070	GM12878	blood:	n/a	n/a
14	TBP	chr1:147012853-147013769	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr1:147012880-147013030	HCPEpiC	choroid plexus:	n/a	n/a
16	RUNX3	chr1:147012721-147013476	GM12878	blood:	n/a	n/a
17	MYC	chr1:147012883-147013236	HUVEC	blood vessel:	n/a	n/a
18	TCF7L2	chr1:147012747-147013436	HCT-116	colon:	n/a	chr1:147013311-147013327 chr1:147013315-147013325 chr1:147013312-147013326 chr1:147013315-147013324 chr1:147013311-147013327
19	CTCF	chr1:147012838-147013027	Fibrobl	skin:	n/a	n/a
20	CTCF	chr1:147012806-147013056	Lung_OC	lung:	n/a	n/a
21	JUND	chr1:147011993-147014293	SK-N-SH	brain:	n/a	n/a
22	TCF7L2	chr1:147012841-147013413	PANC-1	pancreas:	n/a	chr1:147013311-147013327 chr1:147013315-147013325 chr1:147013312-147013326 chr1:147013315-147013324 chr1:147013311-147013327
23	EP300	chr1:147012986-147013468	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:147012551-147014384	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr1:147012293-147014261	H1-hESC	embryonic stem cell:	n/a	n/a
26	SP1	chr1:147012601-147013528	A549	lung:	n/a	chr1:147012821-147012830
27	MAZ	chr1:147012403-147014639	IMR90	lung:	n/a	n/a
28	BHLHE40	chr1:147012843-147013503	K562	blood:	n/a	n/a
29	POLR2A	chr1:147012637-147013723	HEK293	kidney:	n/a	n/a
30	MAFK	chr1:147012993-147013497	H1-hESC	embryonic stem cell:	n/a	chr1:147013159-147013170
31	EP300	chr1:147012996-147013502	H1-hESC	embryonic stem cell:	n/a	n/a
32	KAP1	chr1:147012548-147014307	HEK293	kidney:	n/a	n/a
33	CTCF	chr1:147012845-147013031	ProgFib	skin:	n/a	n/a
34	TAF1	chr1:147012511-147014342	H1-neurons	neurons:	n/a	n/a
35	TAF1	chr1:147012615-147013644	SK-N-SH	brain:	n/a	n/a
36	SP4	chr1:147012984-147013450	H1-hESC	embryonic stem cell:	n/a	n/a
37	YY1	chr1:147012627-147013391	SK-N-SH_RA	brain:	n/a	chr1:147012761-147012771 chr1:147012760-147012772
38	MAX	chr1:147012561-147013482	A549	lung:	n/a	n/a
39	POLR2A	chr1:147012697-147013361	HCT-116	colon:	n/a	n/a
40	RCOR1	chr1:147012523-147013258	K562	blood:	n/a	n/a
41	REST	chr1:147012681-147013418	PFSK-1	brain:	n/a	n/a
42	MAX	chr1:147012627-147013443	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr1:147012682-147013526	HUVEC	blood vessel:	n/a	n/a
44	TEAD4	chr1:147012639-147013438	ECC-1	luminal epithelium:	n/a	n/a
45	TAF1	chr1:147012690-147013062	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr1:147012555-147014046	ECC-1	luminal epithelium:	n/a	n/a
47	CHD1	chr1:147011883-147015001	IMR90	lung:	n/a	n/a
48	TCF7L2	chr1:147012700-147013455	Hela-S3	cervix:	n/a	chr1:147013311-147013327 chr1:147013315-147013325 chr1:147013312-147013326 chr1:147013315-147013324 chr1:147013311-147013327
49	RAD21	chr1:147012639-147013343	SK-N-SH_RA	brain:	n/a	n/a
50	PBX3	chr1:147012616-147013380	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:147011744..147014234-chr1:147070783..147073063,3	K562	blood:
2	chr1:147012761..147015831-chr1:147068894..147072363,4	MCF-7	breast:
3	chr1:147011744..147014234-chr1:147070783..147072314,2	K562	blood:
4	chr1:147008733..147014706-chr1:147069097..147075030,9	MCF-7	breast:
5	chr1:147010483..147014086-chr1:147140786..147143809,3	MCF-7	breast:

Variant related genes	Relation type
BCL9	TF binding region
ENSG00000162836	Chromatin interaction
ENSG00000116128	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11240079	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12069005	0.89[EUR][1000 genomes]
rs12072533	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12075087	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17160340	0.85[EUR][1000 genomes]
rs1989733	0.89[EUR][1000 genomes]
rs57710974	0.89[EUR][1000 genomes]
rs58718844	0.89[EUR][1000 genomes]
rs59594924	0.89[EUR][1000 genomes]
rs6668185	0.93[YRI][hapmap]
rs716703	1.00[CEU][hapmap]
rs74125727	0.89[EUR][1000 genomes]
rs7526630	0.85[EUR][1000 genomes]
rs7526706	0.89[EUR][1000 genomes]
rs7554146	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking 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 miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv831414	chr1:146884994-147083866	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv482606	chr1:146959127-147134517	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147010000-147013200	Enhancers	Hela-S3	cervix
2	chr1:147011200-147013200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:147011400-147013200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:147011800-147013200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:147012000-147013200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:147012000-147013400	Weak transcription	Small Intestine	intestine
7	chr1:147012000-147014000	Flanking Active TSS	Dnd41	blood
8	chr1:147012000-147014800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:147012000-147015000	Active TSS	Fetal Kidney	kidney
10	chr1:147012200-147013400	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr1:147012200-147014800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr1:147012400-147013400	Flanking Active TSS	HepG2	liver
13	chr1:147012400-147014600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:147012400-147014800	Active TSS	Aorta	Aorta
15	chr1:147012400-147014800	Active TSS	Right Atrium	heart
16	chr1:147012400-147015000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:147012400-147015000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:147012400-147015200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:147012400-147015200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:147012400-147015200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:147012600-147013200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:147012600-147013200	Enhancers	Fetal Brain Male	brain
23	chr1:147012600-147013200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:147012600-147013400	Active TSS	Brain Germinal Matrix	brain
25	chr1:147012600-147014200	Active TSS	H9 Cell Line	embryonic stem cell
26	chr1:147012600-147014200	Active TSS	Brain Substantia Nigra	brain
27	chr1:147012600-147014400	Active TSS	Left Ventricle	heart
28	chr1:147012600-147014400	Active TSS	Lung	lung
29	chr1:147012600-147014400	Active TSS	Psoas Muscle	Psoas
30	chr1:147012600-147014600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:147012600-147014600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:147012600-147014600	Active TSS	Right Ventricle	heart
33	chr1:147012600-147014800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:147012600-147015200	Active TSS	Ovary	ovary
35	chr1:147012800-147013200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:147012800-147013200	Enhancers	Primary B cells from cord blood	blood
37	chr1:147012800-147013200	Enhancers	Primary T cells from cord blood	blood
38	chr1:147012800-147013200	Active TSS	Primary hematopoietic stem cells	blood
39	chr1:147012800-147013200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:147012800-147013200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:147012800-147013200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:147012800-147013200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:147012800-147013200	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr1:147012800-147013200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:147012800-147013200	Active TSS	HUVEC	blood vessel
46	chr1:147012800-147013200	Enhancers	NHEK	skin
47	chr1:147012800-147013400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:147012800-147013400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:147012800-147013400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:147012800-147013400	Active TSS	Liver	Liver

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