Variant report

Variant	rs3923579
Chromosome Location	chr6:146230232-146230233
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146133273..146135855-chr6:146228681..146230376,2	K562	blood:
2	chr6:146223883..146226442-chr6:146227329..146230872,3	K562	blood:

Extended variants
information (count: 166 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10223508	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10457793	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10457794	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10457795	0.80[ASN][1000 genomes]
rs1062067	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1062068	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10872580	0.81[ASN][1000 genomes]
rs10872582	0.82[EUR][1000 genomes]
rs11155452	0.80[ASN][1000 genomes]
rs1133832	0.96[EUR][1000 genomes]
rs11755334	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11760	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12194437	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12199362	0.81[ASN][1000 genomes]
rs13198450	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1331636	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331637	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331645	0.80[EUR][1000 genomes]
rs1832362	0.81[EUR][1000 genomes]
rs1986729	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2073287	0.83[EUR][1000 genomes]
rs2144478	0.82[EUR][1000 genomes]
rs2207785	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2224120	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2224121	0.86[EUR][1000 genomes]
rs2243665	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2246334	0.92[ASN][1000 genomes]
rs2247206	0.97[EUR][1000 genomes]
rs2247211	0.97[EUR][1000 genomes]
rs2247317	0.88[EUR][1000 genomes]
rs2247429	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247666	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249147	0.81[EUR][1000 genomes]
rs2249386	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250387	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2253194	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2253307	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2253654	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2253764	0.85[EUR][1000 genomes]
rs2253768	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2253880	0.85[EUR][1000 genomes]
rs2253886	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2253887	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2254257	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2254283	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2254288	0.96[EUR][1000 genomes]
rs2256998	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2265467	0.88[EUR][1000 genomes]
rs2265468	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2265469	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265471	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265472	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265474	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2265477	0.88[EUR][1000 genomes]
rs2265915	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2265916	0.81[EUR][1000 genomes]
rs2265917	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265918	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2265919	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2328709	0.81[ASN][1000 genomes]
rs2328712	0.86[EUR][1000 genomes]
rs2474356	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2485632	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2492855	0.85[EUR][1000 genomes]
rs2748482	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748483	0.86[EUR][1000 genomes]
rs2748484	0.86[EUR][1000 genomes]
rs2748485	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2748499	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2748502	0.87[EUR][1000 genomes]
rs2777476	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2777477	0.87[EUR][1000 genomes]
rs2777484	0.86[EUR][1000 genomes]
rs2814866	0.86[EUR][1000 genomes]
rs2814867	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2814869	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814874	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814875	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814876	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814877	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814879	0.85[EUR][1000 genomes]
rs2814880	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2892453	0.82[EUR][1000 genomes]
rs3811102	0.81[ASN][1000 genomes]
rs3924498	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924499	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924502	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075694	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075695	0.87[EUR][1000 genomes]
rs4075696	0.87[EUR][1000 genomes]
rs4243478	0.86[EUR][1000 genomes]
rs4280983	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4314514	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4316025	0.89[EUR][1000 genomes]
rs4360151	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4391282	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4435956	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4566902	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4896852	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56181683	0.88[EUR][1000 genomes]
rs62435810	0.91[ASN][1000 genomes]
rs6570723	0.81[EUR][1000 genomes]
rs6570724	0.81[EUR][1000 genomes]
rs6570736	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6906258	0.81[ASN][1000 genomes]
rs6906402	0.81[ASN][1000 genomes]
rs6910790	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6914813	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6915718	0.81[ASN][1000 genomes]
rs6917135	0.81[EUR][1000 genomes]
rs6917482	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6922507	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6923545	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924159	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926076	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6926657	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6930975	0.82[EUR][1000 genomes]
rs6931553	0.81[ASN][1000 genomes]
rs6938972	0.80[ASN][1000 genomes]
rs7739418	0.83[EUR][1000 genomes]
rs7742333	0.81[EUR][1000 genomes]
rs7745696	0.81[EUR][1000 genomes]
rs7747576	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7753092	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753696	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755440	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7762562	0.81[EUR][1000 genomes]
rs854145	0.83[EUR][1000 genomes]
rs864390	0.87[EUR][1000 genomes]
rs866473	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322043	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322046	0.81[EUR][1000 genomes]
rs9322047	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs932522	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9373475	0.81[ASN][1000 genomes]
rs9373485	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9376968	0.81[EUR][1000 genomes]
rs9376970	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376971	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9376975	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9386132	0.81[ASN][1000 genomes]
rs9386134	0.81[ASN][1000 genomes]
rs9386141	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9390356	0.81[ASN][1000 genomes]
rs9390365	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390377	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9399567	0.81[EUR][1000 genomes]
rs9399569	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9399571	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9403749	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403755	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9403756	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9403757	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9403764	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403765	0.82[EUR][1000 genomes]
rs9403767	0.80[ASN][1000 genomes]
rs9497424	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9497425	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9497427	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9497431	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9497434	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9497435	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9791313	0.86[AMR][1000 genomes];0.95[EUR][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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv437525	chr6:146212285-146230454	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3923579	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146201200-146230400	Weak transcription	NHEK	skin
2	chr6:146207800-146240200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:146210200-146231000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:146210400-146230400	Weak transcription	NH-A	brain
5	chr6:146210400-146282000	Weak transcription	Spleen	Spleen
6	chr6:146211600-146236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:146213800-146230400	Weak transcription	HUVEC	blood vessel
8	chr6:146215000-146242200	Weak transcription	Hela-S3	cervix
9	chr6:146219200-146249200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:146219200-146276600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:146219600-146250600	Strong transcription	Dnd41	blood
12	chr6:146219800-146271400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:146220000-146231400	Weak transcription	Aorta	Aorta
14	chr6:146220000-146249400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:146220000-146255200	Weak transcription	Gastric	stomach
16	chr6:146220000-146259400	Weak transcription	Esophagus	oesophagus
17	chr6:146220000-146276800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:146220000-146283200	Weak transcription	Small Intestine	intestine
19	chr6:146220200-146231400	Weak transcription	Thymus	Thymus
20	chr6:146220200-146231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:146220200-146268400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:146220400-146255200	Weak transcription	Fetal Intestine Small	intestine
23	chr6:146221800-146230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:146223800-146248600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:146224600-146257000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:146224800-146233200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:146224800-146235800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:146224800-146235800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:146224800-146235800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:146224800-146237200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr6:146225000-146230600	Weak transcription	NHDF-Ad	bronchial
32	chr6:146225200-146233400	Strong transcription	Ovary	ovary
33	chr6:146225200-146268600	Weak transcription	Stomach Mucosa	stomach
34	chr6:146225400-146235000	Strong transcription	Brain Germinal Matrix	brain
35	chr6:146225400-146248400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:146225400-146249600	Strong transcription	Adipose Nuclei	Adipose
37	chr6:146225600-146235800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:146225600-146237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:146225800-146233600	Strong transcription	Fetal Lung	lung
40	chr6:146225800-146235600	Strong transcription	Placenta	Placenta
41	chr6:146225800-146243800	Weak transcription	Psoas Muscle	Psoas
42	chr6:146226000-146233200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:146226000-146249000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:146226000-146249600	Strong transcription	Liver	Liver
45	chr6:146226200-146284200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:146226400-146231200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:146226400-146231400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:146226400-146231400	Weak transcription	Right Ventricle	heart
49	chr6:146226400-146231600	Strong transcription	Fetal Brain Male	brain
50	chr6:146226400-146232000	Strong transcription	Brain Angular Gyrus	brain

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