Variant report

Variant	rs13195636
Chromosome Location	chr6:27509493-27509494
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27495180..27505101-chr6:27505644..27514408,17	K562	blood:
2	chr6:27114696..27118355-chr6:27509086..27513263,4	K562	blood:
3	chr6:27488952..27490702-chr6:27508233..27510472,2	K562	blood:
4	chr6:27507279..27509804-chr6:27513834..27516409,2	MCF-7	breast:
5	chr6:27488952..27490638-chr6:27507376..27509733,2	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13191227	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13191474	0.91[EUR][1000 genomes]
rs13192965	0.85[EUR][1000 genomes]
rs13195040	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs13196692	0.83[EUR][1000 genomes]
rs13202775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13207689	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13218537	0.83[EUR][1000 genomes]
rs17749927	0.85[EUR][1000 genomes]
rs28360634	0.81[EUR][1000 genomes]
rs34064842	0.83[EUR][1000 genomes]
rs34071253	0.82[EUR][1000 genomes]
rs34105070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34196306	0.90[EUR][1000 genomes]
rs34332556	0.83[EUR][1000 genomes]
rs34409918	0.83[EUR][1000 genomes]
rs34432857	0.83[EUR][1000 genomes]
rs34573979	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34613987	0.89[EUR][1000 genomes]
rs34864796	0.89[EUR][1000 genomes]
rs34953377	0.83[EUR][1000 genomes]
rs34965299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35120058	0.83[EUR][1000 genomes]
rs35715914	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35716472	0.82[EUR][1000 genomes]
rs35848276	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35984974	0.82[EUR][1000 genomes]
rs41269265	0.91[EUR][1000 genomes]
rs56405707	0.85[EUR][1000 genomes]
rs58616630	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs66785117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66841633	0.83[EUR][1000 genomes]
rs67240003	0.89[EUR][1000 genomes]
rs67652222	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67859638	0.85[EUR][1000 genomes]
rs6904596	0.89[EUR][1000 genomes]
rs6918792	0.87[EUR][1000 genomes]
rs71559038	0.83[EUR][1000 genomes]
rs72839477	0.81[EUR][1000 genomes]
rs72845046	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845070	0.85[EUR][1000 genomes]
rs7749305	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13195636	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13195636	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13195636	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27501400-27511600	Weak transcription	HMEC	breast
2	chr6:27507000-27510000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27507600-27509600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:27508000-27509600	Weak transcription	HepG2	liver
5	chr6:27508000-27511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:27508800-27510000	Flanking Active TSS	K562	blood
7	chr6:27509000-27509800	Active TSS	A549	lung
8	chr6:27509000-27510000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:27509200-27509800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:27509200-27510000	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:27509200-27510000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:27509200-27510000	Enhancers	Hela-S3	cervix
13	chr6:27509200-27512400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:27509400-27509600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:27509400-27509800	Active TSS	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links