Variant report

Variant	rs7657269
Chromosome Location	chr4:147102663-147102664
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	chr4:147100998..147102686-chr4:147106253..147108281,2	K562	blood:
2	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10000407	0.84[EUR][1000 genomes]
rs10519776	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723069	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11725678	0.83[EUR][1000 genomes]
rs11728525	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11728609	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940961	0.82[EUR][1000 genomes]
rs12152657	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021186	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756056	0.84[EUR][1000 genomes]
rs17756234	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864371	0.83[EUR][1000 genomes]
rs1865531	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007366	0.84[EUR][1000 genomes]
rs2068009	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393640	0.83[EUR][1000 genomes]
rs28420466	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756081	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756083	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3948408	0.83[EUR][1000 genomes]
rs4282199	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549398	0.83[EUR][1000 genomes]
rs4835286	0.83[EUR][1000 genomes]
rs55736910	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56279747	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289966	0.83[EUR][1000 genomes]
rs56331233	0.81[AMR][1000 genomes]
rs56333123	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326764	0.83[EUR][1000 genomes]
rs62326797	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326802	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62326804	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326851	0.81[AMR][1000 genomes]
rs6537399	0.83[EUR][1000 genomes]
rs6537400	0.84[EUR][1000 genomes]
rs6537401	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832576	0.84[EUR][1000 genomes]
rs6838458	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844381	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727922	0.83[EUR][1000 genomes]
rs72727944	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs72727960	0.81[AMR][1000 genomes]
rs7665079	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.84[EUR][1000 genomes]
rs7745	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7657269	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7657269	RP11-6L6.2	cis	Artery Tibial	GTEx
rs7657269	RP11-6L6.2	cis	lung	GTEx
rs7657269	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs7657269	RP11-6L6.2	cis	Whole Blood	GTEx
rs7657269	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147097600-147108800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:147097800-147104200	Weak transcription	Placenta	Placenta
3	chr4:147097800-147104600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:147097800-147108600	Weak transcription	HSMMtube	muscle
5	chr4:147097800-147108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:147097800-147108800	Weak transcription	Esophagus	oesophagus
7	chr4:147097800-147111000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:147097800-147115400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:147098000-147102800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:147098400-147103200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:147098400-147103600	Weak transcription	A549	lung
12	chr4:147098400-147104200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:147098400-147104400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:147098400-147107400	Weak transcription	HSMM	muscle
15	chr4:147098400-147107800	Weak transcription	Fetal Kidney	kidney
16	chr4:147098400-147108000	Weak transcription	NH-A	brain
17	chr4:147098400-147108800	Weak transcription	NHLF	lung
18	chr4:147098400-147111400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
20	chr4:147098600-147103600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:147098600-147103600	Weak transcription	NHDF-Ad	bronchial
22	chr4:147098600-147103800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:147098600-147103800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:147098600-147104000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:147098600-147104200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:147098600-147104200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr4:147098600-147104400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:147098600-147105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:147098600-147107800	Weak transcription	HMEC	breast
30	chr4:147098600-147113800	Weak transcription	Hela-S3	cervix
31	chr4:147099000-147104400	Weak transcription	Fetal Intestine Large	intestine
32	chr4:147099000-147108400	Weak transcription	Aorta	Aorta
33	chr4:147099200-147107400	Weak transcription	Osteobl	bone
34	chr4:147099200-147107600	Weak transcription	Brain Germinal Matrix	brain
35	chr4:147099400-147104200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:147099400-147104200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr4:147099400-147107800	Weak transcription	Thymus	Thymus
38	chr4:147099400-147108000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:147099400-147108200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:147099400-147109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:147099600-147103800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:147099600-147104400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:147099800-147103600	Weak transcription	K562	blood
44	chr4:147099800-147104200	Weak transcription	Fetal Thymus	thymus
45	chr4:147100000-147103800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:147100000-147103800	Weak transcription	Primary B cells from cord blood	blood
47	chr4:147100000-147107800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:147100200-147107800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:147100200-147108800	Weak transcription	Fetal Stomach	stomach
50	chr4:147100200-147108800	Weak transcription	HUVEC	blood vessel

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