Variant report

Variant	rs7415756
Chromosome Location	chr1:169334282-169334283
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	STAT3	chr1:169334121-169334647	MCF10A-Er-Src	breast:	n/a	n/a
2	KAP1	chr1:169334257-169334554	K562	blood:	n/a	n/a
3	POLR2A	chr1:169334215-169334598	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:169334204-169334562	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:169334140-169334621	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:169334179-169334675	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:169334162-169334573	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr1:169334138-169334661	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:169334102-169334644	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:169334230-169334456	Hela-S3	cervix:	n/a	n/a
11	CBX3	chr1:169334230-169334679	K562	blood:	n/a	n/a
12	STAT3	chr1:169334206-169334534	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr1:169334215-169334534	MCF10A-Er-Src	breast:	n/a	n/a
14	MAFK	chr1:169334269-169334356	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169324847..169326824-chr1:169332989..169335675,2	K562	blood:
3	chr1:169332852..169334456-chr1:169336922..169338977,2	MCF-7	breast:

Variant related genes	Relation type
BLZF1	TF binding region
ENSG00000143156	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1018831	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs10429893	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10753786	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs10800408	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs10800424	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10800425	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10800435	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10800438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800439	0.85[CEU][hapmap]
rs10800440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919124	0.89[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10919132	0.85[CEU][hapmap];0.96[YRI][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap]
rs1124843	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	0.89[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap]
rs1200085	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12029566	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208370	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1208377	0.89[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1400836	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1591733	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs16861990	0.82[JPT][hapmap]
rs1856303	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1914505	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983546	0.82[JPT][hapmap]
rs2003653	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	0.85[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2138898	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176474	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300158	0.86[CEU][hapmap];0.96[YRI][hapmap]
rs3766057	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs3766095	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs3820059	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3905328	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4454599	0.83[AMR][1000 genomes]
rs4656183	0.86[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656672	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6427187	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.82[JPT][hapmap]
rs6669901	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700375	0.81[ASN][1000 genomes]
rs7533257	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7535765	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7544221	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7415756	NME7	cis	Artery Aorta	GTEx
rs7415756	NME7	cis	Nerve Tibial	GTEx
rs7415756	NME7	cis	Artery Tibial	GTEx
rs7415756	NME7	cis	Stomach	GTEx
rs7415756	NME7	cis	Esophagus Muscularis	GTEx
rs7415756	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs7415756	NME7	cis	Thyroid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309400-169336400	Weak transcription	Ovary	ovary
4	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
6	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
7	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:169325600-169335800	Weak transcription	K562	blood
9	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
10	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
12	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
14	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:169331600-169335600	Enhancers	HMEC	breast
16	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:169332000-169334400	Enhancers	NHEK	skin
19	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:169332800-169334600	Enhancers	Placenta	Placenta
22	chr1:169332800-169334800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:169332800-169336400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:169333000-169334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:169333000-169336000	Weak transcription	NHDF-Ad	bronchial
26	chr1:169333000-169336200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:169333000-169336200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:169333000-169336200	Weak transcription	Thymus	Thymus
29	chr1:169333200-169334400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:169333200-169335800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:169333200-169335800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:169333200-169335800	Weak transcription	NHLF	lung
33	chr1:169333200-169336000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:169333200-169336200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:169333200-169336200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:169333200-169336200	Weak transcription	Fetal Stomach	stomach
37	chr1:169333200-169336200	Enhancers	Hela-S3	cervix
38	chr1:169333200-169336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:169333200-169336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:169333400-169335800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:169333400-169335800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:169333400-169336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:169333400-169336000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:169333400-169336000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:169333400-169336000	Weak transcription	HUVEC	blood vessel
47	chr1:169333400-169336200	Weak transcription	Osteobl	bone
48	chr1:169333600-169334800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr1:169333600-169335600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:169333600-169335600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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