Variant report

Variant	rs3807864
Chromosome Location	chr7:12250573-12250574
allele	A/C
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	REST	chr7:12250538-12251259	A549	lung:	n/a	chr7:12250989-12251009 chr7:12251155-12251168 chr7:12251158-12251171 chr7:12250992-12251005 chr7:12251001-12251010 chr7:12251035-12251045
2	POLR2A	chr7:12250224-12251340	K562	blood:	n/a	n/a
3	POU2F2	chr7:12250559-12251266	GM12878	blood:	n/a	n/a
4	TAF1	chr7:12250458-12251328	Hela-S3	cervix:	n/a	n/a
5	PML	chr7:12250544-12251363	MCF-7	breast:	n/a	n/a
6	MYC	chr7:12250345-12251439	NB4	blood:	n/a	chr7:12250959-12250969
7	MXI1	chr7:12250092-12251432	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:12250226-12251452	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr7:12250465-12251631	GM12878	blood:	n/a	n/a
10	SIX5	chr7:12250350-12251250	A549	lung:	n/a	n/a
11	POLR2A	chr7:12250526-12251192	K562	blood:	n/a	n/a
12	GATA3	chr7:12249761-12251069	T-47D	breast:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
13	POLR2A	chr7:12250341-12251392	U87	brain:	n/a	n/a
14	MYBL2	chr7:12250390-12251588	HepG2	liver:	n/a	n/a
15	MAX	chr7:12250418-12251462	HepG2	liver:	n/a	chr7:12250959-12250969
16	MXI1	chr7:12250104-12251573	Hela-S3	cervix:	n/a	n/a
17	RCOR1	chr7:12250318-12251547	K562	blood:	n/a	n/a
18	POLR2A	chr7:12249858-12251921	Hela-S3	cervix:	n/a	n/a
19	NRF1	chr7:12249916-12251408	SK-N-SH	brain:	n/a	chr7:12250843-12250854 chr7:12250843-12250857 chr7:12250840-12250854 chr7:12250842-12250853 chr7:12250843-12250852
20	PML	chr7:12250240-12251378	GM12878	blood:	n/a	n/a
21	TCF7L2	chr7:12250148-12250925	MCF-7	breast:	n/a	chr7:12250703-12250713
22	CREB1	chr7:12250258-12251492	HepG2	liver:	n/a	n/a
23	TFAP2C	chr7:12250167-12251414	Hela-S3	cervix:	n/a	n/a
24	CCNT2	chr7:12250488-12251334	K562	blood:	n/a	chr7:12250905-12250914
25	FOS	chr7:12250472-12250962	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr7:12250237-12251538	H1-hESC	embryonic stem cell:	n/a	chr7:12250959-12250969
27	SETDB1	chr7:12250229-12251279	K562	blood:	n/a	chr7:12250844-12250853
28	TRIM28	chr7:12250432-12251260	K562	blood:	n/a	n/a
29	ZNF263	chr7:12250371-12251603	HEK293-T-REx	kidney:	n/a	n/a
30	TCF12	chr7:12250413-12251127	A549	lung:	n/a	n/a
31	ATF3	chr7:12250371-12251061	A549	lung:	n/a	n/a
32	TCF12	chr7:12250314-12251626	ECC-1	luminal epithelium:	n/a	n/a
33	RCOR1	chr7:12250437-12251357	HepG2	liver:	n/a	n/a
34	MAX	chr7:12250432-12251443	K562	blood:	n/a	chr7:12250959-12250969
35	KAP1	chr7:12250060-12252083	HEK293	kidney:	n/a	chr7:12251695-12251703
36	POLR2A	chr7:12250561-12251252	HUVEC	blood vessel:	n/a	n/a
37	FOSL2	chr7:12250440-12250914	A549	lung:	n/a	n/a
38	TAF1	chr7:12250416-12251486	ECC-1	luminal epithelium:	n/a	n/a
39	USF1	chr7:12250513-12250972	SK-N-SH_RA	brain:	n/a	n/a
40	POLR2A	chr7:12250402-12251392	U87	brain:	n/a	n/a
41	TAF1	chr7:12250468-12251385	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr7:12250548-12251398	K562	blood:	n/a	n/a
43	POLR2A	chr7:12250497-12251385	MCF-7	breast:	n/a	n/a
44	USF2	chr7:12250550-12250986	GM12878	blood:	n/a	n/a
45	CHD2	chr7:12250270-12251344	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr7:12250529-12251190	A549	lung:	n/a	n/a
47	MAX	chr7:12250226-12251600	ECC-1	luminal epithelium:	n/a	chr7:12250959-12250969
48	CREB1	chr7:12250530-12251399	H1-hESC	embryonic stem cell:	n/a	n/a
49	FOSL2	chr7:12250508-12251411	A549	lung:	n/a	n/a
50	SRF	chr7:12250439-12251391	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12248340..12250610-chr7:12341759..12344659,2	K562	blood:
2	chr20:44563231..44563776-chr7:12249962..12250824,2	Hela-S3	cervix:
3	chr7:12245428..12248475-chr7:12248558..12250664,3	K562	blood:
4	chr7:12237815..12240381-chr7:12248250..12250812,3	K562	blood:

Variant related genes	Relation type
TMEM106B	TF binding region
ENSG00000100982	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17594223	0.86[EUR][1000 genomes]
rs17595150	0.92[EUR][1000 genomes]
rs17595402	0.98[EUR][1000 genomes]
rs17665337	0.98[EUR][1000 genomes]
rs60495893	0.98[EUR][1000 genomes]
rs73299019	0.98[EUR][1000 genomes]
rs73299021	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73299040	0.87[AMR][1000 genomes];1.00[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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1021710	chr7:12164993-12251790	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12249600-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:12249800-12250600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr7:12249800-12250600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr7:12249800-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:12249800-12250800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr7:12249800-12251000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:12249800-12251200	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr7:12249800-12251400	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr7:12249800-12251400	Active TSS	Fetal Brain Female	brain
10	chr7:12249800-12251600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:12249800-12251600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr7:12249800-12251600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:12249800-12251600	Active TSS	Brain Angular Gyrus	brain
14	chr7:12249800-12251600	Active TSS	Brain Substantia Nigra	brain
15	chr7:12249800-12251600	Active TSS	Duodenum Mucosa	Duodenum
16	chr7:12249800-12251600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr7:12249800-12251600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr7:12249800-12251600	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr7:12249800-12251600	Active TSS	Stomach Smooth Muscle	stomach
20	chr7:12249800-12251600	Active TSS	NH-A	brain
21	chr7:12249800-12251800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:12249800-12251800	Active TSS	Brain Cingulate Gyrus	brain
23	chr7:12249800-12251800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:12249800-12252000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:12249800-12252200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:12249800-12252200	Active TSS	Right Atrium	heart
27	chr7:12249800-12253000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr7:12250000-12251000	Active TSS	Primary T cells fromperipheralblood	blood
29	chr7:12250000-12251200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:12250000-12251200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:12250000-12251400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr7:12250000-12251400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:12250000-12251600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:12250000-12251600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:12250000-12251600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:12250000-12251600	Active TSS	Liver	Liver
37	chr7:12250000-12251600	Active TSS	Colon Smooth Muscle	Colon
38	chr7:12250000-12251600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr7:12250000-12251600	Active TSS	Fetal Intestine Small	intestine
40	chr7:12250000-12251600	Active TSS	Fetal Lung	lung
41	chr7:12250000-12251600	Active TSS	Placenta	Placenta
42	chr7:12250000-12251600	Active TSS	Fetal Stomach	stomach
43	chr7:12250000-12251600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr7:12250000-12251600	Active TSS	Psoas Muscle	Psoas
45	chr7:12250000-12251600	Active TSS	Stomach Mucosa	stomach
46	chr7:12250000-12251600	Active TSS	Thymus	Thymus
47	chr7:12250000-12251600	Active TSS	Hela-S3	cervix
48	chr7:12250000-12251600	Active TSS	HSMMtube	muscle
49	chr7:12250000-12251600	Active TSS	NHEK	skin
50	chr7:12250000-12251800	Active TSS	H1 Cell Line	embryonic stem cell

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