Variant report

Variant	rs778715
Chromosome Location	chr7:65849209-65849210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65578865..65581340-chr7:65848179..65850812,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1000464	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10224872	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10228885	0.86[EUR][1000 genomes]
rs10240949	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10250544	0.86[EUR][1000 genomes]
rs10255397	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10256544	0.87[EUR][1000 genomes]
rs10257911	0.84[EUR][1000 genomes]
rs10260426	0.87[EUR][1000 genomes]
rs10261398	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10263690	0.87[EUR][1000 genomes]
rs10276077	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10282433	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10447522	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10807703	0.87[ASN][1000 genomes]
rs10807704	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083554	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10950033	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11760844	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11763189	0.82[EUR][1000 genomes]
rs11764589	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11765791	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11769079	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11773628	0.82[EUR][1000 genomes]
rs11984115	0.86[EUR][1000 genomes]
rs12531677	0.87[EUR][1000 genomes]
rs12534500	0.82[EUR][1000 genomes]
rs12537823	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12668005	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12698522	0.83[AFR][1000 genomes]
rs12698526	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13226170	0.81[AFR][1000 genomes]
rs13230545	0.87[EUR][1000 genomes]
rs13309935	0.86[EUR][1000 genomes]
rs1532571	0.87[EUR][1000 genomes]
rs1643375	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1695820	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1875057	0.87[EUR][1000 genomes]
rs1968225	0.81[AMR][1000 genomes]
rs2036263	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088653	0.88[EUR][1000 genomes]
rs2088655	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2420608	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2420611	0.81[AFR][1000 genomes]
rs28491091	0.83[EUR][1000 genomes]
rs28714531	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2901152	0.86[EUR][1000 genomes]
rs2901155	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2901209	0.82[EUR][1000 genomes]
rs2909688	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3857685	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3893216	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4078376	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4149461	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4236208	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4587224	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4623294	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718324	0.80[EUR][1000 genomes]
rs4718328	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718329	0.81[EUR][1000 genomes]
rs4718330	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4718343	0.80[AMR][1000 genomes]
rs4718344	0.80[AMR][1000 genomes]
rs4718356	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57739047	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460278	0.83[EUR][1000 genomes]
rs6460279	0.83[EUR][1000 genomes]
rs6460282	0.84[EUR][1000 genomes]
rs6460284	0.87[EUR][1000 genomes]
rs6460287	0.86[EUR][1000 genomes]
rs6460290	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6460293	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6460301	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460302	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460303	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6460304	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6944374	0.84[EUR][1000 genomes]
rs6945775	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6951503	0.87[EUR][1000 genomes]
rs6952182	0.84[EUR][1000 genomes]
rs6952473	0.80[EUR][1000 genomes]
rs6958294	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6959268	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6960446	0.87[EUR][1000 genomes]
rs6961990	0.82[AFR][1000 genomes]
rs6962717	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6963228	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6964437	0.84[EUR][1000 genomes]
rs6971752	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974614	0.83[EUR][1000 genomes]
rs6976714	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6978028	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6979452	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6980451	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs709596	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7778322	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7781880	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7782704	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783779	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs778680	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778684	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778686	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778690	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs778694	0.80[AMR][1000 genomes]
rs778697	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs778700	0.81[AMR][1000 genomes]
rs778702	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778703	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778705	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778706	0.81[AMR][1000 genomes]
rs778707	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778709	0.87[AFR][1000 genomes]
rs778710	0.80[AMR][1000 genomes]
rs778711	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778712	0.82[AMR][1000 genomes]
rs778716	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778719	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs778720	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778724	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778728	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778734	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778736	0.88[EUR][1000 genomes]
rs7788984	0.80[AFR][1000 genomes]
rs7789615	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7796162	0.85[EUR][1000 genomes]
rs7798630	0.87[EUR][1000 genomes]
rs7799834	0.80[AMR][1000 genomes]
rs7803424	0.80[AMR][1000 genomes]
rs809025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs880166	0.86[EUR][1000 genomes]
rs949930	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	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	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking 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	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv970513	chr7:65842694-65860742	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981506	chr7:65842694-65876873	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs778715	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs778715	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs778715	LINC00174	cis	Thyroid	GTEx
rs778715	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs778715	RNU6-96P	cis	Thyroid	GTEx
rs778715	RP4-756H11.3	cis	Thyroid	GTEx
rs778715	GTF2IRD1P1	cis	Thyroid	GTEx
rs778715	RP4-756H11.3	cis	Artery Aorta	GTEx
rs778715	RP4-756H11.3	cis	lung	GTEx
rs778715	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs778715	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs778715	GS1-124K5.2	cis	Whole Blood	GTEx
rs778715	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs778715	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs778715	GS1-124K5.11	cis	Thyroid	GTEx
rs778715	GS1-124K5.4	cis	Stomach	GTEx
rs778715	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs778715	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs778715	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs778715	RP4-756H11.3	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65840000-65878400	Weak transcription	Psoas Muscle	Psoas
2	chr7:65840400-65873400	Weak transcription	K562	blood
3	chr7:65840600-65858400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:65841400-65875400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:65842400-65867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:65843400-65877600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:65843600-65878200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:65843800-65851000	Weak transcription	GM12878-XiMat	blood
9	chr7:65844000-65878400	Weak transcription	Thymus	Thymus
10	chr7:65844600-65860400	Weak transcription	Esophagus	oesophagus
11	chr7:65845000-65856000	Weak transcription	Right Atrium	heart
12	chr7:65845000-65866800	Weak transcription	Brain Anterior Caudate	brain
13	chr7:65845000-65867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:65845000-65867200	Weak transcription	Spleen	Spleen
15	chr7:65845000-65873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:65845000-65873600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:65845000-65878000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:65845000-65878000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:65845000-65878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:65845000-65878200	Weak transcription	Right Ventricle	heart
21	chr7:65845000-65878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:65845000-65878400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr7:65845000-65878400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:65845200-65850000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:65845200-65850400	Weak transcription	Lung	lung
26	chr7:65845200-65856200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:65845200-65867200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr7:65845200-65873400	Weak transcription	HepG2	liver
29	chr7:65845200-65878200	Weak transcription	Left Ventricle	heart
30	chr7:65845200-65878600	Weak transcription	Aorta	Aorta
31	chr7:65845400-65853600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:65845400-65854200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:65845400-65856400	Weak transcription	Fetal Intestine Large	intestine
34	chr7:65845400-65860400	Weak transcription	Osteobl	bone
35	chr7:65845400-65863400	Weak transcription	Brain Angular Gyrus	brain
36	chr7:65845400-65864200	Weak transcription	Primary T cells from cord blood	blood
37	chr7:65845400-65865600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:65845400-65866600	Weak transcription	Adipose Nuclei	Adipose
39	chr7:65845400-65875400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:65845400-65877200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:65845400-65878000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:65845400-65878200	Weak transcription	Brain Germinal Matrix	brain
43	chr7:65845400-65878200	Weak transcription	Pancreas	Pancrea
44	chr7:65845600-65849600	Weak transcription	HUVEC	blood vessel
45	chr7:65845600-65849800	Weak transcription	NHEK	skin
46	chr7:65845600-65850000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:65845600-65855800	Weak transcription	Fetal Intestine Small	intestine
48	chr7:65845600-65857200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:65845600-65860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:65845600-65864000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links