Variant report

Variant	rs11971949
Chromosome Location	chr7:65626014-65626015
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	chr7:65617048..65619822-chr7:65625013..65626809,2	MCF-7	breast:
2	chr7:65625074..65627224-chr7:65631943..65634316,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10215948	0.81[EUR][1000 genomes]
rs10240249	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10247043	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10253922	0.85[AFR][1000 genomes]
rs10256544	0.81[AFR][1000 genomes]
rs10257427	0.81[EUR][1000 genomes]
rs10267430	0.80[EUR][1000 genomes]
rs10271553	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10272021	0.84[ASN][1000 genomes]
rs1129531	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1144894	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1144895	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1167390	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1167395	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1167411	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1167612	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1182882	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1183245	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11974219	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11974264	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13225383	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13240492	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13245728	0.87[AFR][1000 genomes]
rs13247295	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13309935	0.81[AFR][1000 genomes]
rs1540651	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1565531	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs160635	0.83[AMR][1000 genomes]
rs1612452	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1616988	0.82[AMR][1000 genomes]
rs1976200	0.87[AFR][1000 genomes]
rs1983372	0.86[AMR][1000 genomes]
rs2087647	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2173570	0.81[EUR][1000 genomes]
rs2220626	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2249458	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2420168	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420173	0.94[AFR][1000 genomes]
rs2420174	0.94[AFR][1000 genomes]
rs28391294	0.86[AFR][1000 genomes]
rs28470208	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs28682868	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2949696	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35028832	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35034167	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3935391	0.80[EUR][1000 genomes]
rs427557	0.81[AMR][1000 genomes]
rs427575	0.81[AMR][1000 genomes]
rs4368860	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4612218	0.83[AMR][1000 genomes]
rs4718319	0.94[AFR][1000 genomes]
rs55748098	0.80[EUR][1000 genomes]
rs55962648	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57866200	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59466412	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6945843	0.81[EUR][1000 genomes]
rs6946143	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6957690	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6958484	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6961717	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6963646	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6967708	0.91[AFR][1000 genomes]
rs6971509	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6977501	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs697968	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs697969	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs697970	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs709608	0.82[AMR][1000 genomes]
rs709609	0.81[AMR][1000 genomes]
rs7782806	0.91[AFR][1000 genomes]
rs7786892	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7801282	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs780742	0.88[AMR][1000 genomes]
rs780743	0.90[AMR][1000 genomes]
rs780744	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7809814	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs780998	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs809080	0.83[AMR][1000 genomes]
rs875971	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908915	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs937495	0.80[EUR][1000 genomes]
rs9969301	0.80[EUR][1000 genomes]
rs9986696	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv971172	chr7:65616238-65653268	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11971949	RP4-756H11.3	cis	lung	GTEx
rs11971949	GS1-124K5.4	cis	Artery Aorta	GTEx
rs11971949	GS1-124K5.11	cis	Thyroid	GTEx
rs11971949	RP4-756H11.3	cis	Artery Aorta	GTEx
rs11971949	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs11971949	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs11971949	RNU6-96P	cis	Thyroid	GTEx
rs11971949	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs11971949	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs11971949	GS1-124K5.4	cis	Whole Blood	GTEx
rs11971949	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs11971949	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs11971949	GTF2IRD1P1	cis	Thyroid	GTEx
rs11971949	RP4-756H11.3	cis	Thyroid	GTEx
rs11971949	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11971949	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs11971949	RP4-756H11.3	cis	Artery Tibial	GTEx
rs11971949	GS1-124K5.4	cis	Stomach	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65612000-65635400	Weak transcription	Fetal Kidney	kidney
2	chr7:65617600-65628800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:65617600-65632400	Weak transcription	Hela-S3	cervix
4	chr7:65618200-65632400	Weak transcription	HUVEC	blood vessel
5	chr7:65618200-65635400	Weak transcription	Esophagus	oesophagus
6	chr7:65618200-65635600	Weak transcription	Right Ventricle	heart
7	chr7:65618800-65627600	Weak transcription	NHEK	skin
8	chr7:65619000-65627800	Weak transcription	HepG2	liver
9	chr7:65619000-65631200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:65619000-65632400	Weak transcription	NHLF	lung
11	chr7:65619000-65632800	Weak transcription	Gastric	stomach
12	chr7:65619000-65635200	Weak transcription	Spleen	Spleen
13	chr7:65619000-65635400	Weak transcription	Pancreas	Pancrea
14	chr7:65619000-65635600	Weak transcription	HMEC	breast
15	chr7:65619000-65635800	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:65619400-65632400	Weak transcription	NHDF-Ad	bronchial
17	chr7:65620800-65635400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:65621000-65627800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:65622400-65632800	Weak transcription	Brain Substantia Nigra	brain
20	chr7:65622600-65635600	Weak transcription	Stomach Mucosa	stomach
21	chr7:65622800-65632600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:65623600-65626400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:65623600-65627000	Weak transcription	Primary B cells from cord blood	blood
24	chr7:65623600-65627200	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:65623600-65627800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:65623600-65630400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:65623600-65632400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:65623600-65633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65623600-65635400	Weak transcription	Colonic Mucosa	Colon
30	chr7:65623600-65635600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:65623800-65626600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:65623800-65626600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:65623800-65626800	Weak transcription	Placenta	Placenta
34	chr7:65623800-65627000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:65623800-65627000	Weak transcription	Thymus	Thymus
36	chr7:65623800-65627400	Weak transcription	Primary T cells from cord blood	blood
37	chr7:65623800-65627800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:65623800-65627800	Weak transcription	Liver	Liver
39	chr7:65623800-65629600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:65623800-65632600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:65623800-65632600	Weak transcription	A549	lung
42	chr7:65623800-65632800	Weak transcription	NH-A	brain
43	chr7:65623800-65632800	Weak transcription	Osteobl	bone
44	chr7:65623800-65633000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:65623800-65633000	Weak transcription	K562	blood
46	chr7:65623800-65635400	Weak transcription	Adipose Nuclei	Adipose
47	chr7:65623800-65635400	Weak transcription	Lung	lung
48	chr7:65623800-65635400	Weak transcription	Ovary	ovary
49	chr7:65623800-65635400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr7:65623800-65635400	Weak transcription	HSMMtube	muscle

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