Variant report

Variant	rs316313
Chromosome Location	chr7:65593548-65593549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65586822..65589395-chr7:65593306..65595408,2	MCF-7	breast:

Extended variants
information (count: 165 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1039664	0.82[AMR][1000 genomes]
rs1061361	0.84[AMR][1000 genomes]
rs10807699	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1134256	0.81[AMR][1000 genomes]
rs11538349	0.81[AMR][1000 genomes]
rs1167613	0.82[AMR][1000 genomes]
rs1177514	0.82[AMR][1000 genomes]
rs12698509	0.82[AMR][1000 genomes]
rs13226598	0.82[AMR][1000 genomes]
rs13308751	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546059	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs160543	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160639	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160642	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160643	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160644	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160646	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160648	0.91[AMR][1000 genomes]
rs160649	0.91[AMR][1000 genomes]
rs160651	0.91[AMR][1000 genomes]
rs160652	0.93[AMR][1000 genomes]
rs160655	0.91[AMR][1000 genomes]
rs160656	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs160657	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1626926	0.82[AMR][1000 genomes]
rs1701745	0.82[AMR][1000 genomes]
rs1701750	0.82[AMR][1000 genomes]
rs1701758	0.82[AMR][1000 genomes]
rs1701759	0.82[AMR][1000 genomes]
rs1715235	0.84[AMR][1000 genomes]
rs1723265	0.82[AMR][1000 genomes]
rs1723266	0.84[AMR][1000 genomes]
rs1723267	0.84[AMR][1000 genomes]
rs1723269	0.84[AMR][1000 genomes]
rs1723270	0.84[AMR][1000 genomes]
rs1723272	0.82[AMR][1000 genomes]
rs182600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873494	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs188765	0.84[AMR][1000 genomes]
rs1964692	0.84[AMR][1000 genomes]
rs2243480	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257790	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420170	0.82[AMR][1000 genomes]
rs2420171	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2420172	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2456483	0.82[AMR][1000 genomes]
rs2460422	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460425	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460426	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460431	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2462569	0.82[AMR][1000 genomes]
rs2465120	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2637561	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2658583	0.84[AMR][1000 genomes]
rs2949697	0.82[AMR][1000 genomes]
rs2961102	0.84[AMR][1000 genomes]
rs3105600	0.84[AMR][1000 genomes]
rs313798	0.84[AMR][1000 genomes]
rs313799	0.82[AMR][1000 genomes]
rs313800	0.82[AMR][1000 genomes]
rs313801	0.89[AMR][1000 genomes]
rs313802	0.89[AMR][1000 genomes]
rs313803	0.89[AMR][1000 genomes]
rs313807	0.82[AMR][1000 genomes]
rs313809	0.84[AMR][1000 genomes]
rs313813	0.85[AMR][1000 genomes]
rs313814	0.85[AMR][1000 genomes]
rs313819	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313821	0.95[ASN][1000 genomes]
rs313822	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313831	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313832	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313833	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316304	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316315	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs316317	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316318	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316321	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316322	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316325	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316329	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316331	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316332	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs316334	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34032527	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34970380	0.84[AMR][1000 genomes]
rs35268390	0.81[AMR][1000 genomes]
rs35396113	0.84[AMR][1000 genomes]
rs35542501	0.81[AMR][1000 genomes]
rs35679560	0.82[AMR][1000 genomes]
rs36004293	0.81[AMR][1000 genomes]
rs36084489	0.84[AMR][1000 genomes]
rs36127118	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs387676	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs392355	0.84[AMR][1000 genomes]
rs402418	0.85[AMR][1000 genomes]
rs403089	0.89[AMR][1000 genomes]
rs4145008	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs419603	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422164	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423187	0.84[AMR][1000 genomes]
rs427044	0.84[AMR][1000 genomes]
rs431076	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431318	0.85[AMR][1000 genomes]
rs437889	0.85[AMR][1000 genomes]
rs4481472	0.84[AMR][1000 genomes]
rs448377	0.84[AMR][1000 genomes]
rs451396	0.84[AMR][1000 genomes]
rs458291	0.87[AMR][1000 genomes]
rs462853	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs465359	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs466983	0.87[AMR][1000 genomes]
rs4718309	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718315	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718316	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4718317	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55886244	0.82[AMR][1000 genomes]
rs57126451	0.82[AMR][1000 genomes]
rs58207111	0.82[AMR][1000 genomes]
rs59794892	0.81[AMR][1000 genomes]
rs59966766	0.84[AMR][1000 genomes]
rs6460274	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6460277	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6958289	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6959002	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6966322	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6974723	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs709607	0.82[AMR][1000 genomes]
rs73136349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73148097	0.84[AMR][1000 genomes]
rs73150014	0.84[AMR][1000 genomes]
rs7787230	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7804223	0.85[AMR][1000 genomes]
rs780453	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs781141	0.81[AMR][1000 genomes]
rs781142	0.82[AMR][1000 genomes]
rs781149	0.82[AMR][1000 genomes]
rs781150	0.84[AMR][1000 genomes]
rs781153	0.84[AMR][1000 genomes]
rs781154	0.84[AMR][1000 genomes]
rs781155	0.84[AMR][1000 genomes]
rs781156	0.84[AMR][1000 genomes]
rs781157	0.82[AMR][1000 genomes]
rs906134	0.82[AMR][1000 genomes]
rs937108	0.82[AMR][1000 genomes]
rs958550	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9769882	0.88[AFR][1000 genomes];0.89[AMR][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv511363	chr7:65587537-65597341	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv607408	chr7:65590561-65599196	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv971489	chr7:65590579-65614004	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv607413	chr7:65591081-65599196	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs316313	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs316313	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs316313	ASL	cis	multi-tissue	Pritchard
rs316313	GUSB	cis	Whole Blood	GTEx
rs316313	RP4-756H11.3	cis	lung	GTEx
rs316313	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs316313	VKORC1L1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65580600-65600600	Weak transcription	Aorta	Aorta
2	chr7:65580800-65606800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:65581000-65595600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:65581000-65595600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:65581000-65595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:65581000-65597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:65581200-65596000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:65581400-65595400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:65581400-65595800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:65581400-65596400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:65581600-65604800	Weak transcription	Colonic Mucosa	Colon
13	chr7:65581800-65595200	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:65581800-65595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:65581800-65595800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:65582000-65595200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:65582000-65595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:65582400-65608200	Weak transcription	Fetal Brain Male	brain
19	chr7:65582600-65595000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr7:65582600-65596400	Weak transcription	NH-A	brain
21	chr7:65583000-65594400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:65583000-65596000	Weak transcription	Thymus	Thymus
23	chr7:65583600-65593600	Weak transcription	Primary B cells from cord blood	blood
24	chr7:65584400-65594400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:65584400-65596000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr7:65584600-65593800	Weak transcription	Fetal Intestine Large	intestine
27	chr7:65584600-65594800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:65584600-65595800	Weak transcription	Spleen	Spleen
29	chr7:65584600-65596000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:65584600-65596000	Weak transcription	Colon Smooth Muscle	Colon
31	chr7:65584600-65596000	Weak transcription	Esophagus	oesophagus
32	chr7:65584600-65596200	Weak transcription	Brain Angular Gyrus	brain
33	chr7:65584600-65596200	Weak transcription	Brain Germinal Matrix	brain
34	chr7:65584600-65597000	Weak transcription	HMEC	breast
35	chr7:65584800-65594600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:65584800-65594800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:65584800-65595200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:65584800-65595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr7:65584800-65595600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr7:65584800-65595800	Weak transcription	A549	lung
41	chr7:65584800-65596200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:65585400-65596200	Weak transcription	NHEK	skin
43	chr7:65585400-65604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr7:65587000-65595200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:65587000-65595400	Weak transcription	Fetal Thymus	thymus
46	chr7:65587000-65595800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:65587000-65596400	Weak transcription	Fetal Kidney	kidney
48	chr7:65587200-65594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:65587200-65595600	Weak transcription	Dnd41	blood
50	chr7:65587400-65595200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links