Variant report

Variant	rs2087647
Chromosome Location	chr7:65593188-65593189
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65590686..65593391-chr7:66020104..66022935,2	K562	blood:
2	chr7:65578668..65580540-chr7:65591809..65593353,2	K562	blood:

Variant related genes	Relation type
ENSG00000177418	Chromatin interaction
ENSG00000241258	Chromatin interaction
ENSG00000232491	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1000464	0.93[CEU][hapmap]
rs10215948	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs10224872	0.92[CEU][hapmap]
rs10228885	0.93[CEU][hapmap]
rs10240249	0.81[AMR][1000 genomes]
rs10247043	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10256544	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs10257427	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10260426	0.92[CEU][hapmap]
rs10261398	0.92[CEU][hapmap]
rs10267430	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10268656	0.81[AMR][1000 genomes]
rs10271553	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10272021	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10282433	0.92[CEU][hapmap]
rs1129531	0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs1144894	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1144895	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1167390	0.92[CEU][hapmap];0.82[CHB][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1167395	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1167406	0.93[CEU][hapmap]
rs1167411	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1167612	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760844	0.93[CEU][hapmap]
rs1182882	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1183245	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11971949	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11974219	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11974264	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11984115	0.92[CEU][hapmap]
rs12537823	0.92[CEU][hapmap]
rs13225383	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13240492	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13247295	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1540651	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1565531	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs160635	0.82[AMR][1000 genomes]
rs1612452	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1616988	0.81[AMR][1000 genomes]
rs1875057	0.92[CEU][hapmap]
rs1983372	0.92[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2173570	1.00[CEU][hapmap]
rs2220626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2249458	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs2420168	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28470208	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28682868	0.81[AMR][1000 genomes]
rs2901152	0.92[CEU][hapmap]
rs2949696	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35028832	0.91[AMR][1000 genomes]
rs35034167	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4149461	0.92[CEU][hapmap]
rs4236208	0.92[CEU][hapmap]
rs4368860	0.85[AMR][1000 genomes]
rs4612218	0.82[AMR][1000 genomes]
rs4718330	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs55962648	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57866200	0.84[AMR][1000 genomes]
rs587360	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs59466412	0.84[AMR][1000 genomes]
rs6460282	0.92[CEU][hapmap]
rs6944374	0.88[CEU][hapmap]
rs6945843	1.00[CEU][hapmap]
rs6946143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951503	0.89[CEU][hapmap]
rs6952182	0.92[CEU][hapmap]
rs6957690	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6960446	0.92[CEU][hapmap]
rs6961717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6963646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6964437	0.92[CEU][hapmap]
rs6971509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6974614	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs697968	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs697969	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs697970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs709608	0.81[AMR][1000 genomes]
rs709609	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7786892	0.85[AMR][1000 genomes]
rs7794930	1.00[CEU][hapmap]
rs7798630	0.93[CEU][hapmap]
rs7801282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780742	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs780743	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs780744	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7809814	0.86[AMR][1000 genomes]
rs780998	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs809080	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs875971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs880166	0.93[CEU][hapmap]
rs908915	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes]
rs937495	1.00[CEU][hapmap]
rs949930	0.93[CEU][hapmap]
rs9986696	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv3477313	chr7:65588417-65593415	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2087647	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs2087647	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2087647	GTF2IRD1P1	cis	Thyroid	GTEx
rs2087647	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2087647	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2087647	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2087647	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2087647	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2087647	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2087647	RP4-756H11.3	cis	Artery Aorta	GTEx
rs2087647	RP4-756H11.3	cis	Thyroid	GTEx
rs2087647	GS1-124K5.4	cis	Stomach	GTEx
rs2087647	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2087647	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2087647	GS1-124K5.4	cis	Whole Blood	GTEx
rs2087647	RP4-756H11.3	cis	lung	GTEx
rs2087647	GS1-124K5.11	cis	Thyroid	GTEx
rs2087647	RNU6-96P	cis	Thyroid	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

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