Variant report

Variant	rs9260862
Chromosome Location	chr6:29945741-29945742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29855991..29858588-chr6:29944087..29945954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230521	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs2232239	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2894000	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3734832	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823364	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823372	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823384	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3901554	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60466513	0.86[ASN][1000 genomes]
rs6903621	0.86[ASN][1000 genomes]
rs6924054	0.86[ASN][1000 genomes]
rs9260391	0.85[AMR][1000 genomes]
rs9260497	0.85[AMR][1000 genomes]
rs9260569	0.85[AMR][1000 genomes]
rs9260733	0.83[EUR][1000 genomes]
rs9260736	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9260768	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9260828	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260830	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260837	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260860	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260861	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260863	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260864	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260865	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260867	0.83[EUR][1000 genomes]
rs9260868	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260869	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260870	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260871	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9260909	0.82[ASN][1000 genomes]
rs9260914	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260915	0.83[ASN][1000 genomes]
rs9260916	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260917	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260918	0.86[ASN][1000 genomes]
rs9260919	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260921	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260923	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260929	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260930	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260931	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260932	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260933	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9260935	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260936	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260938	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260939	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260941	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260943	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260946	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260948	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260950	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260954	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260957	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260958	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9260976	0.86[ASN][1000 genomes]
rs9260981	0.86[ASN][1000 genomes]
rs9260984	0.86[ASN][1000 genomes]
rs9260986	0.86[ASN][1000 genomes]
rs9260998	0.86[ASN][1000 genomes]
rs9261005	0.86[ASN][1000 genomes]
rs9261025	0.86[ASN][1000 genomes]
rs9261027	0.82[ASN][1000 genomes]
rs9261028	0.86[ASN][1000 genomes]
rs9261029	0.86[ASN][1000 genomes]
rs9261035	0.86[ASN][1000 genomes]
rs9261036	0.86[ASN][1000 genomes]
rs9261037	0.86[ASN][1000 genomes]
rs9261040	0.86[ASN][1000 genomes]
rs9261041	0.86[ASN][1000 genomes]
rs9261042	0.86[ASN][1000 genomes]
rs9261043	0.82[ASN][1000 genomes]
rs9261044	0.86[ASN][1000 genomes]
rs9261045	0.86[ASN][1000 genomes]
rs9261046	0.86[ASN][1000 genomes]
rs9261056	0.82[ASN][1000 genomes]
rs9261059	0.82[ASN][1000 genomes]
rs9261063	0.82[ASN][1000 genomes]
rs9261065	0.82[ASN][1000 genomes]
rs9261066	0.82[ASN][1000 genomes]
rs9261068	0.82[ASN][1000 genomes]
rs9261069	0.82[ASN][1000 genomes]
rs9261070	0.82[ASN][1000 genomes]
rs9261071	0.82[ASN][1000 genomes]
rs9261072	0.82[ASN][1000 genomes]
rs9261073	0.82[ASN][1000 genomes]
rs9261075	0.82[ASN][1000 genomes]
rs9261076	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
21	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
22	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv511863	chr6:29945557-29948665	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9260862	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9260862	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29945000-29945800	Bivalent Enhancer	Fetal Heart	heart
2	chr6:29945000-29945800	Flanking Active TSS	K562	blood
3	chr6:29945200-29945800	Enhancers	Liver	Liver
4	chr6:29945200-29948600	Weak transcription	Small Intestine	intestine
5	chr6:29945200-29948600	Weak transcription	Spleen	Spleen
6	chr6:29945400-29945800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:29945400-29945800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:29945400-29945800	Enhancers	Fetal Intestine Small	intestine
9	chr6:29945400-29945800	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr6:29945400-29945800	Enhancers	A549	lung
11	chr6:29945400-29948800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:29945400-29950200	Weak transcription	Right Atrium	heart
13	chr6:29945600-29945800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:29945600-29945800	Enhancers	HepG2	liver
15	chr6:29945600-29948000	Weak transcription	Colonic Mucosa	Colon
16	chr6:29945600-29948600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:29945600-29948600	Weak transcription	Stomach Mucosa	stomach
18	chr6:29945600-29948800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:29945600-29966400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links