Variant report

Variant	rs3135327
Chromosome Location	chr6:28913922-28913923
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	chr6:28913503..28915110-chr6:28972198..28974208,2	MCF-7	breast:
2	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-17	chr6:28913625-28914076	NONHSAT108498

Variant related genes	Relation type
ENSG00000197935	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000263426	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1002925	0.85[EUR][1000 genomes]
rs1005123	0.81[ASN][1000 genomes]
rs1237485	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476016	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169683	0.82[EUR][1000 genomes]
rs1794587	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs184093	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2006173	0.83[EUR][1000 genomes]
rs2013848	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2032500	0.87[EUR][1000 genomes]
rs2071785	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2071790	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209122	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209126	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209128	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209129	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209137	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs209138	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs209148	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs209149	0.86[EUR][1000 genomes]
rs209152	0.84[EUR][1000 genomes]
rs209153	0.87[EUR][1000 genomes]
rs209160	0.84[EUR][1000 genomes]
rs209161	0.87[EUR][1000 genomes]
rs209163	0.87[EUR][1000 genomes]
rs209164	0.84[EUR][1000 genomes]
rs209171	0.81[EUR][1000 genomes]
rs209173	0.82[EUR][1000 genomes]
rs209175	0.81[EUR][1000 genomes]
rs209176	0.85[EUR][1000 genomes]
rs209179	0.82[EUR][1000 genomes]
rs209184	0.83[EUR][1000 genomes]
rs209186	0.82[EUR][1000 genomes]
rs2157312	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2157313	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2187807	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2187808	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2208536	0.82[EUR][1000 genomes]
rs2269555	0.82[ASN][1000 genomes]
rs2754764	0.82[EUR][1000 genomes]
rs2754767	0.82[EUR][1000 genomes]
rs2765218	0.81[EUR][1000 genomes]
rs2765219	0.82[EUR][1000 genomes]
rs2765229	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3129792	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129793	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130841	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130842	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3130886	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3130889	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130897	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131070	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3131074	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131077	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3131100	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3131102	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3131342	0.82[EUR][1000 genomes]
rs3132386	0.85[EUR][1000 genomes]
rs3135303	0.87[EUR][1000 genomes]
rs3135315	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135319	0.81[EUR][1000 genomes]
rs3135321	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135322	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3135323	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135324	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135326	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3135328	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs377392	0.83[EUR][1000 genomes]
rs381808	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs386628	0.83[EUR][1000 genomes]
rs393431	0.85[EUR][1000 genomes]
rs4427026	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4713186	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4713187	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4713188	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4713190	0.84[ASN][1000 genomes]
rs4713192	0.84[ASN][1000 genomes]
rs4947339	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs526983	0.82[EUR][1000 genomes]
rs6456876	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6456880	0.83[ASN][1000 genomes]
rs6456883	0.82[ASN][1000 genomes]
rs6901599	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6904975	0.82[ASN][1000 genomes]
rs6906909	0.82[ASN][1000 genomes]
rs6914955	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6916161	0.82[ASN][1000 genomes]
rs6920392	0.84[ASN][1000 genomes]
rs6931823	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs763009	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7743189	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7761547	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9257401	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9257404	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9257405	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9257408	0.81[ASN][1000 genomes]
rs9257421	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9257447	0.83[ASN][1000 genomes]
rs9257449	0.83[ASN][1000 genomes]
rs9257455	0.80[ASN][1000 genomes]
rs9257461	0.82[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	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28915000	Weak transcription	Stomach Mucosa	stomach
2	chr6:28912200-28915200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:28912200-28915600	Weak transcription	Pancreas	Pancrea
4	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:28912400-28914200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:28912400-28914200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:28912400-28914800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:28912400-28915000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:28912400-28915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:28912400-28915200	Weak transcription	Colonic Mucosa	Colon
11	chr6:28912400-28915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:28912400-28915400	Weak transcription	Esophagus	oesophagus
15	chr6:28912400-28915400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:28912400-28915400	Weak transcription	A549	lung
17	chr6:28912400-28915400	Weak transcription	HUVEC	blood vessel
18	chr6:28912400-28915400	Weak transcription	NHEK	skin
19	chr6:28912400-28915600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:28912400-28915600	Weak transcription	HMEC	breast
21	chr6:28912400-28915800	Weak transcription	NH-A	brain
22	chr6:28912400-28915800	Weak transcription	Osteobl	bone
23	chr6:28912400-28916000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:28912400-28916200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:28912400-28916800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
29	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
30	chr6:28912600-28915400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:28912600-28915400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:28912800-28914400	Weak transcription	Hela-S3	cervix
33	chr6:28912800-28915400	Enhancers	HepG2	liver
34	chr6:28912800-28915600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:28912800-28915800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:28912800-28916000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:28913200-28916600	Enhancers	K562	blood
38	chr6:28913400-28915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:28913800-28914000	Enhancers	Spleen	Spleen
40	chr6:28913800-28914800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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