Variant report

Variant	rs2707850
Chromosome Location	chr7:66203870-66203871
allele	G/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	POLR2A	chr7:66203758-66203958	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:66202616-66206527	HepG2	liver:	n/a	n/a
3	ZNF384	chr7:66203702-66203896	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:66201840-66203958	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:66161177..66163221-chr7:66202677..66204246,2	MCF-7	breast:
2	chr7:66192001..66196955-chr7:66201177..66204851,5	K562	blood:
3	chr7:66145819..66148736-chr7:66203770..66205462,3	MCF-7	breast:
4	chr10:81964075..81964667-chr7:66203761..66204300,2	Hela-S3	cervix:

Variant related genes	Relation type
KCTD7	TF binding region
RABGEF1	TF binding region
ENSG00000122359	Chromatin interaction
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10215132	0.89[EUR][1000 genomes]
rs10215516	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10234018	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10249404	0.90[EUR][1000 genomes]
rs10252765	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255377	0.83[EUR][1000 genomes]
rs10263935	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10272357	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10272546	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10274773	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10278371	0.90[EUR][1000 genomes]
rs10278816	0.90[EUR][1000 genomes]
rs10281080	0.90[EUR][1000 genomes]
rs10950044	0.90[EUR][1000 genomes]
rs1110414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11765356	0.90[EUR][1000 genomes]
rs11766262	0.87[EUR][1000 genomes]
rs11768727	0.98[EUR][1000 genomes]
rs11772264	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772636	0.97[EUR][1000 genomes]
rs11773829	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13227951	0.88[EUR][1000 genomes]
rs13239306	0.80[EUR][1000 genomes]
rs1553609	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553610	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17566701	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1860468	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1860470	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1961155	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1968127	0.90[EUR][1000 genomes]
rs2003301	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2013222	0.89[EUR][1000 genomes]
rs2055682	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2191268	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286683	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286684	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2420824	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2420827	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659888	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659899	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659906	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659909	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2659912	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659915	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2659916	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707822	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2707827	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707836	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707841	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707845	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2707848	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2707849	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707852	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707853	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2707854	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2707856	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28698552	0.83[EUR][1000 genomes]
rs28830215	0.90[EUR][1000 genomes]
rs28887326	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3069894	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34356500	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35130766	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35526611	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35986979	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764903	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3778909	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3800820	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3800823	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857686	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3857688	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3898855	0.90[EUR][1000 genomes]
rs4273746	0.83[EUR][1000 genomes]
rs4279493	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4717310	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4717319	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718403	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718405	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56229325	0.87[EUR][1000 genomes]
rs62465434	0.83[EUR][1000 genomes]
rs62466793	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62466794	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467857	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6460305	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460308	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460309	0.82[EUR][1000 genomes]
rs6943696	0.90[EUR][1000 genomes]
rs6949912	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6958520	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6960778	0.92[EUR][1000 genomes]
rs6965056	0.90[EUR][1000 genomes]
rs6979488	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71563125	0.90[EUR][1000 genomes]
rs7357230	0.87[EUR][1000 genomes]
rs7779971	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7782320	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7783924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785213	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7788576	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7789184	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7789419	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793569	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7807930	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7807944	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801190	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs801193	0.89[EUR][1000 genomes]
rs801196	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs801205	0.84[EUR][1000 genomes]
rs801211	0.84[EUR][1000 genomes]
rs801216	0.82[EUR][1000 genomes]
rs801217	0.83[EUR][1000 genomes]
rs810400	0.84[EUR][1000 genomes]
rs9791890	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv971490	chr7:66192193-66212423	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2707850	RP4-756H11.3	cis	Thyroid	GTEx
rs2707850	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2707850	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2707850	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2707850	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2707850	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2707850	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2707850	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2707850	RP4-756H11.3	cis	Stomach	GTEx
rs2707850	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2707850	RP4-756H11.3	cis	lung	GTEx
rs2707850	RP4-756H11.3	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:66176400-66204600	Weak transcription	Colonic Mucosa	Colon
3	chr7:66179600-66204600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:66182800-66205000	Weak transcription	Gastric	stomach
5	chr7:66190400-66204600	Weak transcription	Stomach Mucosa	stomach
6	chr7:66190800-66204400	Weak transcription	Fetal Heart	heart
7	chr7:66190800-66204600	Weak transcription	NHEK	skin
8	chr7:66191200-66204600	Weak transcription	NHLF	lung
9	chr7:66191200-66205000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:66191400-66204600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:66191600-66204600	Weak transcription	NHDF-Ad	bronchial
12	chr7:66191800-66204800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:66193800-66204800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:66194000-66204800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:66194000-66205000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:66194000-66205000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:66194600-66204600	Weak transcription	Fetal Kidney	kidney
18	chr7:66194600-66205000	Weak transcription	Spleen	Spleen
19	chr7:66195600-66204800	Weak transcription	Lung	lung
20	chr7:66197000-66204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr7:66197400-66204600	Weak transcription	Right Ventricle	heart
22	chr7:66199600-66204800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:66200600-66204600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:66200800-66205000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:66201200-66204600	Weak transcription	Fetal Intestine Large	intestine
26	chr7:66201200-66204800	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:66201400-66204200	Weak transcription	Fetal Thymus	thymus
28	chr7:66201400-66204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:66201400-66204600	Weak transcription	Fetal Lung	lung
30	chr7:66201600-66204200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:66201600-66204200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:66201600-66204200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr7:66201600-66204400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:66201600-66204400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:66201600-66204400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:66201600-66204400	Weak transcription	HepG2	liver
37	chr7:66201600-66204600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:66201600-66204600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:66201600-66204600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr7:66201600-66204600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:66201600-66204600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:66201600-66204600	Enhancers	Primary B cells from cord blood	blood
43	chr7:66201600-66204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:66201600-66204600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:66201600-66204600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr7:66201600-66204600	Weak transcription	Colon Smooth Muscle	Colon
47	chr7:66201600-66204600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr7:66201600-66204600	Weak transcription	Fetal Brain Female	brain
49	chr7:66201600-66204600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:66201600-66204600	Weak transcription	Thymus	Thymus

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