Variant report

Variant	rs13194781
Chromosome Location	chr6:27815639-27815640
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	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs13192965	0.83[EUR][1000 genomes]
rs13193295	0.89[EUR][1000 genomes]
rs13193480	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13195728	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13199649	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13200214	0.82[EUR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13210634	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13212651	1.00[CEU][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs13216117	0.96[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13218875	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs149943	0.83[CEU][hapmap]
rs149990	0.83[CEU][hapmap]
rs175597	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs17693963	1.00[CEU][hapmap]
rs17695758	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17749927	0.83[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs188015	0.81[EUR][1000 genomes]
rs200481	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200482	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs200483	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200489	0.86[EUR][1000 genomes]
rs200490	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs200493	0.82[EUR][1000 genomes]
rs200497	0.85[EUR][1000 genomes]
rs200501	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs200948	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200949	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs200950	0.90[EUR][1000 genomes]
rs200952	0.90[EUR][1000 genomes]
rs200953	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs200954	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200977	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200981	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs200983	0.88[EUR][1000 genomes]
rs200989	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200990	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs200992	0.83[EUR][1000 genomes]
rs200995	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs200996	0.88[EUR][1000 genomes]
rs201002	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs202906	0.80[CEU][hapmap]
rs2747054	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs28360499	0.95[EUR][1000 genomes]
rs34064842	0.85[EUR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34295134	0.88[EUR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34706883	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34718920	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34788973	0.96[EUR][1000 genomes]
rs35037868	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes]
rs35339855	1.00[AFR][1000 genomes]
rs35501037	0.89[EUR][1000 genomes]
rs35715914	0.83[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36101351	0.96[EUR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs390764	0.86[EUR][1000 genomes]
rs401754	0.86[EUR][1000 genomes]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs45509595	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs483143	0.88[EUR][1000 genomes]
rs493161	0.90[EUR][1000 genomes]
rs557042	0.90[EUR][1000 genomes]
rs56405707	0.83[EUR][1000 genomes]
rs61742093	0.96[EUR][1000 genomes]
rs66868086	1.00[EUR][1000 genomes]
rs67040724	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs67101035	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71537572	0.89[EUR][1000 genomes]
rs71559038	0.82[EUR][1000 genomes]
rs71559050	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71559051	0.87[AMR][1000 genomes]
rs71559054	0.96[EUR][1000 genomes]
rs72845070	0.83[EUR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9368531	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13194781	LOC100270746	cis	lymphoblastoid	seeQTL
rs13194781	BTN3A2	trans	lymphoblastoid	seeQTL
rs13194781	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs13194781	AL022393.7	cis	Muscle Skeletal	GTEx
rs13194781	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13194781	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27807600-27816600	Weak transcription	Pancreas	Pancrea
2	chr6:27808000-27815800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:27808000-27819000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:27808000-27822400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:27808000-27831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:27808200-27817200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:27808200-27818800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:27808200-27830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:27808400-27818000	Weak transcription	Hela-S3	cervix
10	chr6:27810200-27816800	Strong transcription	K562	blood
11	chr6:27810400-27817800	Weak transcription	Fetal Thymus	thymus
12	chr6:27813800-27822200	Weak transcription	Primary B cells from cord blood	blood
13	chr6:27814000-27822200	Weak transcription	GM12878-XiMat	blood
14	chr6:27814800-27817000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:27815000-27816200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:27815000-27816200	Enhancers	NHDF-Ad	bronchial
17	chr6:27815000-27816600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:27815200-27816000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:27815200-27816000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:27815200-27816200	Enhancers	NHLF	lung
21	chr6:27815200-27816200	Enhancers	Osteobl	bone
22	chr6:27815200-27817000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:27815400-27815800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links