Variant report

Variant	rs10268656
Chromosome Location	chr7:65595217-65595218
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: 58 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10240249	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10253922	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10256544	0.80[AMR][1000 genomes]
rs10271553	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1129531	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1167390	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1167399	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1167406	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1167408	0.85[ASN][1000 genomes]
rs13240492	0.80[AFR][1000 genomes]
rs13242721	0.82[AFR][1000 genomes]
rs13245728	0.85[AFR][1000 genomes]
rs13309935	0.83[AMR][1000 genomes]
rs1612452	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1616988	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1976200	0.85[AFR][1000 genomes]
rs1983372	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2087647	0.81[AMR][1000 genomes]
rs2249458	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420168	0.81[AMR][1000 genomes]
rs2420173	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2420174	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2460430	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2460432	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28391294	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28470208	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2949696	0.81[AFR][1000 genomes]
rs34550048	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35034167	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4368860	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4612218	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4718319	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55962648	0.81[AMR][1000 genomes]
rs57866200	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59466412	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62467451	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946143	0.81[AMR][1000 genomes]
rs6951787	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6957690	0.81[AFR][1000 genomes]
rs6958484	0.81[AMR][1000 genomes]
rs6967708	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs709608	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs709609	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7782806	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7786892	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7801282	0.81[AMR][1000 genomes]
rs7809814	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875971	0.81[AMR][1000 genomes]
rs880166	0.81[AMR][1000 genomes]
rs908915	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9767916	0.86[AMR][1000 genomes];0.83[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	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10268656	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs10268656	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs10268656	RNU6-96P	cis	Thyroid	GTEx
rs10268656	GS1-124K5.4	cis	Artery Aorta	GTEx
rs10268656	GS1-124K5.2	cis	Whole Blood	GTEx
rs10268656	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs10268656	GS1-124K5.11	cis	Thyroid	GTEx
rs10268656	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs10268656	RP4-756H11.3	cis	lung	GTEx
rs10268656	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs10268656	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs10268656	LINC00174	cis	Thyroid	GTEx
rs10268656	GS1-124K5.4	cis	Stomach	GTEx
rs10268656	RP4-756H11.3	cis	Artery Tibial	GTEx
rs10268656	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs10268656	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs10268656	RP4-756H11.3	cis	Thyroid	GTEx
rs10268656	GTF2IRD1P1	cis	Thyroid	GTEx
rs10268656	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr7:65581800-65595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:65581800-65595800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:65582000-65595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:65582400-65608200	Weak transcription	Fetal Brain Male	brain
17	chr7:65582600-65596400	Weak transcription	NH-A	brain
18	chr7:65583000-65596000	Weak transcription	Thymus	Thymus
19	chr7:65584400-65596000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:65584600-65595800	Weak transcription	Spleen	Spleen
21	chr7:65584600-65596000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:65584600-65596000	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:65584600-65596000	Weak transcription	Esophagus	oesophagus
24	chr7:65584600-65596200	Weak transcription	Brain Angular Gyrus	brain
25	chr7:65584600-65596200	Weak transcription	Brain Germinal Matrix	brain
26	chr7:65584600-65597000	Weak transcription	HMEC	breast
27	chr7:65584800-65595600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:65584800-65595800	Weak transcription	A549	lung
29	chr7:65584800-65596200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:65585400-65596200	Weak transcription	NHEK	skin
31	chr7:65585400-65604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:65587000-65595400	Weak transcription	Fetal Thymus	thymus
33	chr7:65587000-65595800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:65587000-65596400	Weak transcription	Fetal Kidney	kidney
35	chr7:65587200-65595600	Weak transcription	Dnd41	blood
36	chr7:65587800-65595600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:65587800-65596200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr7:65587800-65606600	Weak transcription	Stomach Mucosa	stomach
39	chr7:65589800-65595600	Weak transcription	Placenta	Placenta
40	chr7:65589800-65599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:65590000-65596000	Weak transcription	Brain Substantia Nigra	brain
42	chr7:65590000-65596200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:65590000-65597000	Weak transcription	Fetal Brain Female	brain
44	chr7:65590400-65595800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:65590600-65595600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr7:65590600-65596200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr7:65590800-65595600	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:65590800-65595800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:65590800-65595800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr7:65590800-65595800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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