Variant report

Variant	rs160638
Chromosome Location	chr7:65583088-65583089
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65579988..65582211-chr7:65582533..65585744,4	MCF-7	breast:
2	chr7:65578365..65582284-chr7:65582321..65585253,7	MCF-7	breast:
3	chr7:65580634..65584487-chr7:65590516..65592938,4	K562	blood:
4	chr7:65568916..65570554-chr7:65582641..65585238,2	K562	blood:
5	chr7:65581679..65583399-chr7:65586176..65588368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241258	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 6 )

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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546059	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160639	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873494	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[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];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257790	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420170	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2420171	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2420172	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2456483	0.82[AMR][1000 genomes]
rs2460422	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460425	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2460426	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2460431	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2462569	0.82[AMR][1000 genomes]
rs2465120	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316313	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316315	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs316317	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316318	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316321	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs316322	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316325	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316329	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316331	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316332	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs316333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs316334	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34032527	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs387676	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.85[EUR][1000 genomes]
rs419603	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422164	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.97[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];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718315	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718316	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4718317	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[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];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6460277	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6958289	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6959002	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6966322	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6974723	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs709607	0.82[AMR][1000 genomes]
rs73136349	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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];0.85[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];1.00[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];0.85[EUR][1000 genomes]
rs9769882	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs160638	RP4-756H11.3	cis	lung	GTEx
rs160638	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs160638	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs160638	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs160638	GUSB	cis	Whole Blood	GTEx
rs160638	VKORC1L1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65580600-65583200	Enhancers	Spleen	Spleen
2	chr7:65580600-65583400	Enhancers	Stomach Mucosa	stomach
3	chr7:65580600-65584600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:65580600-65584600	Enhancers	Gastric	stomach
5	chr7:65580600-65591000	Weak transcription	Ovary	ovary
6	chr7:65580600-65600600	Weak transcription	Aorta	Aorta
7	chr7:65580800-65583200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:65580800-65583800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:65580800-65584200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:65580800-65606800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:65581000-65583200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:65581000-65583200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:65581000-65583600	Weak transcription	Brain Substantia Nigra	brain
14	chr7:65581000-65583800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr7:65581000-65584000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:65581000-65584000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr7:65581000-65584000	Weak transcription	Right Atrium	heart
18	chr7:65581000-65584200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:65581000-65584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:65581000-65584400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr7:65581000-65584600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:65581000-65587400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:65581000-65589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:65581000-65595600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:65581000-65595600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:65581000-65595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:65581000-65597000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:65581000-65617200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:65581200-65583400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:65581200-65584000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:65581200-65584000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:65581200-65584000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:65581200-65584000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:65581200-65584400	Weak transcription	Placenta	Placenta
35	chr7:65581200-65584800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:65581200-65586200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:65581200-65590200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:65581200-65590600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:65581200-65596000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr7:65581400-65583200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:65581400-65583600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr7:65581400-65583800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr7:65581400-65583800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr7:65581400-65584000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:65581400-65584000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:65581400-65584000	Weak transcription	Brain Angular Gyrus	brain
47	chr7:65581400-65584000	Weak transcription	Brain Germinal Matrix	brain
48	chr7:65581400-65589600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:65581400-65590400	Weak transcription	Osteobl	bone
50	chr7:65581400-65595400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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