Variant report

Variant	rs12531677
Chromosome Location	chr7:65769086-65769087
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	chr7:65767632..65769352-chr7:65774697..65777557,2	K562	blood:

Extended variants
information (count: 123 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1000464	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10224872	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10228885	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10240949	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10250544	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255397	0.90[EUR][1000 genomes]
rs10256544	0.92[EUR][1000 genomes]
rs10257911	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10260426	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10261398	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10263690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272149	0.81[EUR][1000 genomes]
rs10276077	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10282433	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10447522	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807704	0.81[EUR][1000 genomes]
rs1083554	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950033	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11760844	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11764589	0.82[EUR][1000 genomes]
rs11765791	0.85[EUR][1000 genomes]
rs11769079	0.90[EUR][1000 genomes]
rs11984115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534500	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12537823	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12668005	0.83[EUR][1000 genomes]
rs12698522	0.82[EUR][1000 genomes]
rs12698526	0.82[EUR][1000 genomes]
rs13225672	0.83[EUR][1000 genomes]
rs13230545	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13309935	0.91[EUR][1000 genomes]
rs1532571	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643375	0.85[EUR][1000 genomes]
rs1875057	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2036263	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036264	0.86[AFR][1000 genomes]
rs2088653	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2088655	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173570	0.86[AFR][1000 genomes]
rs2420173	0.83[EUR][1000 genomes]
rs2420174	0.83[EUR][1000 genomes]
rs28391294	0.81[EUR][1000 genomes]
rs28491091	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28714531	0.82[EUR][1000 genomes]
rs2901152	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2901155	0.81[EUR][1000 genomes]
rs2909688	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34913718	0.92[EUR][1000 genomes]
rs3857685	0.85[EUR][1000 genomes]
rs3893216	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078376	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4149461	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236208	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587224	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4623294	0.82[EUR][1000 genomes]
rs4718319	0.82[EUR][1000 genomes]
rs4718324	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4718328	0.93[EUR][1000 genomes]
rs4718329	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4718330	0.95[EUR][1000 genomes]
rs6460278	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6460279	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6460282	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6460284	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460287	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460290	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460293	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460303	0.82[EUR][1000 genomes]
rs6944374	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6951503	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6952182	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6952473	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6958294	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959268	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6960446	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6962717	0.84[EUR][1000 genomes]
rs6963228	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6964437	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6967708	0.83[EUR][1000 genomes]
rs6971752	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6974614	0.88[EUR][1000 genomes]
rs6976714	0.84[EUR][1000 genomes]
rs6978028	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6979452	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709596	0.93[EUR][1000 genomes]
rs71526537	0.81[EUR][1000 genomes]
rs7778322	0.81[EUR][1000 genomes]
rs7781880	0.86[EUR][1000 genomes]
rs7782704	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7782806	0.83[EUR][1000 genomes]
rs7783613	0.86[AFR][1000 genomes]
rs7783779	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778680	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs778684	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778686	0.93[EUR][1000 genomes]
rs778690	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778697	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs778702	0.84[EUR][1000 genomes]
rs778703	0.83[EUR][1000 genomes]
rs778705	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs778707	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778711	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs778715	0.87[EUR][1000 genomes]
rs778716	0.87[EUR][1000 genomes]
rs778719	0.81[EUR][1000 genomes]
rs778720	0.87[EUR][1000 genomes]
rs778724	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778728	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs778734	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778736	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787482	0.84[EUR][1000 genomes]
rs7789615	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7794930	0.86[AFR][1000 genomes]
rs7796162	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7798630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs809025	0.87[EUR][1000 genomes]
rs880166	0.91[EUR][1000 genomes]
rs937495	0.86[AFR][1000 genomes]
rs949930	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs12531677	RP4-756H11.3	cis	lung	GTEx
rs12531677	LINC00174	cis	Thyroid	GTEx
rs12531677	RP4-756H11.3	cis	Thyroid	GTEx
rs12531677	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs12531677	GS1-124K5.2	cis	Whole Blood	GTEx
rs12531677	RP4-756H11.3	cis	Artery Tibial	GTEx
rs12531677	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs12531677	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs12531677	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs12531677	GTF2IRD1P1	cis	Thyroid	GTEx
rs12531677	RP4-756H11.3	cis	Whole Blood	GTEx
rs12531677	RNU6-96P	cis	Thyroid	GTEx
rs12531677	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs12531677	GS1-124K5.4	cis	Artery Aorta	GTEx
rs12531677	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs12531677	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12531677	GS1-124K5.11	cis	Thyroid	GTEx
rs12531677	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs12531677	GS1-124K5.4	cis	Stomach	GTEx
rs12531677	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65761600-65772400	Weak transcription	HSMM	muscle
2	chr7:65763000-65769200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:65763000-65770400	Weak transcription	HepG2	liver
4	chr7:65763000-65786200	Weak transcription	Primary B cells from cord blood	blood
5	chr7:65763800-65769400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:65766400-65777600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:65766800-65769800	Enhancers	Fetal Lung	lung
8	chr7:65766800-65780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:65767400-65769800	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr7:65767600-65769600	Enhancers	Colon Smooth Muscle	Colon
11	chr7:65767800-65770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:65767800-65770600	Weak transcription	Ovary	ovary
13	chr7:65767800-65772600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:65768000-65769400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr7:65768000-65780200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:65768200-65769800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:65768200-65769800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:65768200-65771600	Enhancers	NHEK	skin
19	chr7:65768200-65773000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:65768200-65773400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:65768200-65780200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr7:65768400-65769200	Enhancers	Fetal Intestine Large	intestine
23	chr7:65768600-65769400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:65768600-65769400	Enhancers	HUVEC	blood vessel
25	chr7:65768600-65770000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:65768600-65771800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:65768800-65769600	Enhancers	NHLF	lung
28	chr7:65768800-65769800	Enhancers	HMEC	breast
29	chr7:65768800-65770000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:65768800-65770000	Enhancers	Pancreas	Pancrea
31	chr7:65768800-65771600	Enhancers	Fetal Kidney	kidney
32	chr7:65768800-65773600	Enhancers	Stomach Mucosa	stomach
33	chr7:65769000-65769600	Enhancers	Esophagus	oesophagus
34	chr7:65769000-65770200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:65769000-65772800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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