Variant report

Variant	rs9399571
Chromosome Location	chr6:146282061-146282062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146280737..146283631-chr6:146283778..146285950,4	MCF-7	breast:
2	chr6:146280879..146282653-chr6:146284045..146286957,2	MCF-7	breast:
3	chr6:146244640..146248572-chr6:146280738..146282652,3	K562	blood:

Variant related genes	Relation type
ENSG00000146414	Chromatin interaction

Extended variants
information (count: 164 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10223508	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10457792	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10457793	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10457794	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10457795	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1062067	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1062068	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10872582	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10872583	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11155452	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1133832	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11755334	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11760	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12194437	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13198450	0.86[EUR][1000 genomes]
rs13204280	0.81[EUR][1000 genomes]
rs1331636	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1331637	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1331639	0.81[EUR][1000 genomes]
rs1331645	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1412081	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1474871	0.83[EUR][1000 genomes]
rs1832362	0.83[ASN][1000 genomes]
rs1986729	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2073287	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2144477	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2144478	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207785	0.90[EUR][1000 genomes]
rs2224120	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2224121	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2243665	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247206	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247211	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247317	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247429	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2247666	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2249147	0.83[ASN][1000 genomes]
rs2249386	0.82[AFR][1000 genomes]
rs2250387	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253194	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253307	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253648	0.86[ASN][1000 genomes]
rs2253654	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2253764	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253768	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2253880	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253886	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2253887	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2254257	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2254283	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2254288	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2256998	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265467	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265468	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265469	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265471	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265472	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265477	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265915	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2265916	0.83[ASN][1000 genomes]
rs2265917	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265918	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265919	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2328712	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2474356	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2485632	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2492855	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2748482	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2748483	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748484	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748485	0.90[EUR][1000 genomes]
rs2748486	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2748487	0.83[EUR][1000 genomes]
rs2748499	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2748500	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2748502	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777474	0.92[ASN][1000 genomes]
rs2777476	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2777477	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777484	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814866	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814867	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814874	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814875	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814876	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814877	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2814879	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814880	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892453	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3923579	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3924498	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3924499	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3924502	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4075694	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4075695	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4075696	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4243478	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4280983	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4314514	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4316025	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4360151	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4391282	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435956	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4566902	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896852	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56181683	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570736	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6570738	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6908063	0.83[EUR][1000 genomes]
rs6910790	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6913797	0.81[EUR][1000 genomes]
rs6914813	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6917482	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6922507	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6923545	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6924159	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6926076	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6926657	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930975	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6934467	0.82[EUR][1000 genomes]
rs6938972	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7739418	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7740785	0.81[ASN][1000 genomes]
rs7747576	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753092	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7753696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7755440	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs854145	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs864390	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs866473	0.87[EUR][1000 genomes]
rs9322043	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322046	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322047	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9322048	0.83[EUR][1000 genomes]
rs932522	0.86[EUR][1000 genomes]
rs9373485	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9376968	0.83[ASN][1000 genomes]
rs9376970	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9376971	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9376975	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9386141	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390365	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9390377	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9399569	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9399573	0.82[EUR][1000 genomes]
rs9403750	0.81[ASN][1000 genomes]
rs9403755	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9403756	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9403757	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403764	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9403765	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9403767	0.82[EUR][1000 genomes]
rs9403768	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9497424	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497425	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9497427	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497431	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9497434	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9497435	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs969694	0.84[EUR][1000 genomes]
rs9791313	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399571	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	chr6:146220000-146283200	Weak transcription	Small Intestine	intestine
2	chr6:146226200-146284200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:146232000-146282800	Weak transcription	NHLF	lung
4	chr6:146235600-146283800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:146259600-146283200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:146262200-146283400	Weak transcription	Fetal Stomach	stomach
7	chr6:146264800-146284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:146267000-146284200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:146267600-146282600	Weak transcription	Hela-S3	cervix
10	chr6:146268800-146284200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:146268800-146284600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:146269000-146282400	Weak transcription	Stomach Mucosa	stomach
13	chr6:146271000-146284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:146271600-146283400	Weak transcription	HMEC	breast
15	chr6:146271600-146283400	Weak transcription	HSMMtube	muscle
16	chr6:146271600-146283400	Weak transcription	NHDF-Ad	bronchial
17	chr6:146271600-146284200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:146271600-146284600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:146271800-146282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:146271800-146283200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:146271800-146283200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:146271800-146283400	Weak transcription	NH-A	brain
23	chr6:146271800-146284200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:146272000-146283800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:146272000-146284000	Weak transcription	A549	lung
26	chr6:146273000-146283200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:146273200-146283400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:146273200-146283600	Weak transcription	HUVEC	blood vessel
29	chr6:146273200-146284000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:146273200-146284200	Weak transcription	Colonic Mucosa	Colon
31	chr6:146273200-146284400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:146273400-146283200	Weak transcription	Brain Germinal Matrix	brain
33	chr6:146273400-146284000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:146273800-146283200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:146273800-146283200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:146274000-146284200	Weak transcription	HSMM	muscle
37	chr6:146274600-146282200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:146274600-146284600	Weak transcription	Placenta	Placenta
39	chr6:146275600-146284400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:146275800-146282800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:146276000-146283600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:146276000-146283800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:146276000-146283800	Weak transcription	Fetal Kidney	kidney
44	chr6:146276200-146282800	Weak transcription	Primary B cells from cord blood	blood
45	chr6:146276200-146283000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:146276200-146283200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:146276200-146283400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:146276200-146284000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:146276200-146284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:146276400-146282600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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