Variant report

Variant	rs3757556
Chromosome Location	chr7:120590082-120590083
allele	C/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	POLR2A	chr7:120590067-120591521	GM19099	blood:	n/a	n/a
2	TRIM28	chr7:120589790-120591707	K562	blood:	n/a	chr7:120590313-120590321
3	ZNF384	chr7:120590056-120591584	K562	blood:	n/a	n/a
4	POLR2A	chr7:120589913-120590206	K562	blood:	n/a	n/a
5	TBL1XR1	chr7:120589966-120591590	K562	blood:	n/a	n/a
6	POLR2A	chr7:120589988-120591819	IMR90	lung:	n/a	n/a
7	EP300	chr7:120589617-120591850	GM12878	blood:	n/a	chr7:120590757-120590773 chr7:120591530-120591544 chr7:120590997-120591006 chr7:120589917-120589931 chr7:120589789-120589803
8	POLR2A	chr7:120589954-120591647	K562	blood:	n/a	n/a
9	MXI1	chr7:120589208-120592447	SK-N-SH	brain:	n/a	n/a
10	TBP	chr7:120589617-120591658	K562	blood:	n/a	n/a
11	FOXA1	chr7:120589884-120590175	HepG2	liver:	n/a	n/a
12	IRF1	chr7:120589535-120591524	K562	blood:	n/a	chr7:120589835-120589847 chr7:120589916-120589930 chr7:120591181-120591195 chr7:120589917-120589928 chr7:120589788-120589802 chr7:120589915-120589929
13	TEAD4	chr7:120589587-120591737	K562	blood:	n/a	n/a
14	KAP1	chr7:120589614-120590362	K562	blood:	n/a	chr7:120590313-120590321
15	MAZ	chr7:120589708-120591734	IMR90	lung:	n/a	n/a
16	JUN	chr7:120588687-120592316	K562	blood:	n/a	chr7:120591810-120591819
17	RFX5	chr7:120589622-120591601	Hela-S3	cervix:	n/a	chr7:120589815-120589823
18	PML	chr7:120589345-120591757	K562	blood:	n/a	chr7:120590313-120590321
19	TEAD4	chr7:120589232-120591777	K562	blood:	n/a	n/a
20	IRF1	chr7:120589619-120592331	K562	blood:	n/a	chr7:120589835-120589847 chr7:120589916-120589930 chr7:120592151-120592162 chr7:120591181-120591195 chr7:120589917-120589928 chr7:120589788-120589802 chr7:120592109-120592116 chr7:120589915-120589929
21	CBX3	chr7:120590078-120591697	K562	blood:	n/a	n/a
22	EP300	chr7:120589749-120591580	K562	blood:	n/a	chr7:120590757-120590773 chr7:120591530-120591544 chr7:120590997-120591006 chr7:120589917-120589931 chr7:120589789-120589803
23	POLR2A	chr7:120589738-120591620	GM12891	blood:	n/a	n/a
24	MYC	chr7:120589675-120591694	NB4	blood:	n/a	n/a
25	POLR2A	chr7:120590035-120592172	MCF10A-Er-Src	breast:	n/a	n/a
26	PML	chr7:120589606-120591705	K562	blood:	n/a	chr7:120590313-120590321
27	POLR2A	chr7:120589705-120591586	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr7:120590012-120591486	K562	blood:	n/a	n/a
29	ZMIZ1	chr7:120590060-120591710	K562	blood:	n/a	n/a
30	MXI1	chr7:120590021-120591683	K562	blood:	n/a	n/a
31	ARID3A	chr7:120589917-120591920	K562	blood:	n/a	chr7:120590790-120590798
32	POLR2A	chr7:120590080-120591562	GM18951	blood:	n/a	n/a
33	CREB1	chr7:120589978-120591975	K562	blood:	n/a	n/a
34	ZNF143	chr7:120589788-120591471	K562	blood:	n/a	chr7:120590248-120590257 chr7:120590688-120590697 chr7:120590688-120590706 chr7:120590690-120590699 chr7:120590535-120590544
35	POLR2A	chr7:120589882-120591668	K562	blood:	n/a	n/a
36	CEBPB	chr7:120589963-120591675	K562	blood:	n/a	chr7:120591532-120591543
37	RCOR1	chr7:120589469-120591679	K562	blood:	n/a	n/a
38	BCLAF1	chr7:120589911-120591530	K562	blood:	n/a	n/a
39	POLR2A	chr7:120589458-120591769	PBDE	blood:	n/a	n/a
40	CUX1	chr7:120589431-120590627	K562	blood:	n/a	n/a
41	HCFC1	chr7:120589401-120591766	Hela-S3	cervix:	n/a	n/a
42	NFYB	chr7:120589941-120591310	GM12878	blood:	n/a	chr7:120590743-120590758
43	MAX	chr7:120589966-120591694	NB4	blood:	n/a	n/a
44	POLR2A	chr7:120590018-120591656	HepG2	liver:	n/a	n/a
45	CHD1	chr7:120589660-120590084	GM12878	blood:	n/a	n/a
46	RCOR1	chr7:120589541-120591638	Hela-S3	cervix:	n/a	n/a
47	JUND	chr7:120589542-120591564	K562	blood:	n/a	n/a
48	HEY1	chr7:120589889-120591602	K562	blood:	n/a	chr7:120590987-120591002 chr7:120590985-120591000
49	TBP	chr7:120589535-120591537	Hela-S3	cervix:	n/a	n/a
50	MYC	chr7:120589573-120590113	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:120495769..120499665-chr7:120588624..120592417,7	MCF-7	breast:
2	chr7:120380461..120382564-chr7:120588648..120590998,2	K562	blood:
3	chr7:120588429..120592994-chr7:120712560..120717211,6	K562	blood:
4	chr7:120589475..120592677-chr7:120719093..120725846,11	K562	blood:
5	chr7:120588468..120596180-chr7:120604298..120610010,9	MCF-7	breast:
6	chr7:120589600..120593889-chr7:120719099..120726294,8	K562	blood:

Variant related genes	Relation type
ING3	TF binding region
ENSG00000071243	Chromatin interaction
ENSG00000184408	Chromatin interaction
ENSG00000106034	Chromatin interaction
ENSG00000212628	Chromatin interaction
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10225453	0.82[JPT][hapmap]
rs10238554	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10252911	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10257297	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10257475	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10261886	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs10272601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274689	0.82[JPT][hapmap]
rs10282072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10464522	0.82[ASN][1000 genomes]
rs10953922	0.82[ASN][1000 genomes]
rs12154992	1.00[CEU][hapmap]
rs13438082	0.83[ASN][1000 genomes]
rs1557857	0.83[ASN][1000 genomes]
rs17132716	1.00[CEU][hapmap]
rs17142995	0.82[JPT][hapmap]
rs17143055	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs1859316	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859318	0.83[ASN][1000 genomes]
rs1859319	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2074577	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2107276	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2244863	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2244865	0.81[ASN][1000 genomes]
rs2248890	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2525705	0.83[ASN][1000 genomes]
rs2525708	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2525709	0.82[ASN][1000 genomes]
rs2525712	0.81[ASN][1000 genomes]
rs2525713	0.81[ASN][1000 genomes]
rs2525719	0.81[ASN][1000 genomes]
rs2525737	0.81[ASN][1000 genomes]
rs2525743	0.82[ASN][1000 genomes]
rs2721341	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2721347	0.82[JPT][hapmap]
rs2721354	0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2721363	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs2721365	0.81[ASN][1000 genomes]
rs2721367	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs2721372	0.81[ASN][1000 genomes]
rs3757557	1.00[CEU][hapmap]
rs3779386	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs3779387	1.00[CEU][hapmap]
rs3823859	0.81[JPT][hapmap]
rs4141301	1.00[CEU][hapmap]
rs4141309	1.00[CEU][hapmap]
rs41688	0.83[CHB][hapmap]
rs41690	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs4461820	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs6466759	0.82[JPT][hapmap]
rs6466760	0.82[JPT][hapmap]
rs6466761	0.81[JPT][hapmap]
rs6466762	0.81[JPT][hapmap]
rs6953454	0.82[JPT][hapmap]
rs6959328	0.86[JPT][hapmap]
rs6964344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971619	0.81[ASN][1000 genomes]
rs6971854	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6975372	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs6979247	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs732568	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73429803	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs745167	0.82[ASN][1000 genomes]
rs7776721	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7781985	0.81[JPT][hapmap]
rs9649429	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs996903	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS 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	16 gene(s)	inside rSNPs	diseases
2	nsv967472	chr7:120581340-120591647	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120589200-120590200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:120589200-120592000	Active TSS	K562	blood
3	chr7:120589400-120590200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:120589400-120591400	Active TSS	Primary hematopoietic stem cells	blood
5	chr7:120589400-120591400	Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr7:120589400-120592000	Active TSS	Fetal Thymus	thymus
7	chr7:120589400-120592400	Active TSS	A549	lung
8	chr7:120589600-120590200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:120589600-120590200	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr7:120589600-120590200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:120589600-120590200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr7:120589600-120590400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr7:120589600-120590400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr7:120589600-120590600	Active TSS	Right Atrium	heart
15	chr7:120589600-120591200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:120589600-120591200	Active TSS	Rectal Smooth Muscle	rectum
17	chr7:120589600-120591400	Active TSS	Fetal Kidney	kidney
18	chr7:120589600-120591400	Active TSS	NH-A	brain
19	chr7:120589600-120591600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:120589600-120591600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr7:120589600-120591600	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr7:120589600-120591800	Active TSS	H1 Cell Line	embryonic stem cell
23	chr7:120589600-120591800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr7:120589600-120591800	Active TSS	Brain Substantia Nigra	brain
25	chr7:120589600-120591800	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr7:120589600-120592000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr7:120589600-120592000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:120589600-120592000	Active TSS	Thymus	Thymus
29	chr7:120589600-120592000	Active TSS	HepG2	liver
30	chr7:120589600-120592200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr7:120589800-120590200	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr7:120589800-120590200	Flanking Active TSS	Liver	Liver
33	chr7:120589800-120590200	Flanking Active TSS	NHDF-Ad	bronchial
34	chr7:120589800-120590200	Flanking Active TSS	Osteobl	bone
35	chr7:120589800-120590400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr7:120589800-120590400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:120589800-120590400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr7:120589800-120590400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:120589800-120590400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:120589800-120590600	Active TSS	Fetal Heart	heart
41	chr7:120589800-120591200	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr7:120589800-120591400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:120589800-120591400	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr7:120589800-120591400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:120589800-120591400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr7:120589800-120591400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr7:120589800-120591400	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr7:120589800-120591400	Active TSS	HMEC	breast
49	chr7:120589800-120591600	Active TSS	Brain Angular Gyrus	brain
50	chr7:120589800-120591600	Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links