Variant report

Variant	rs200994
Chromosome Location	chr6:27813813-27813814
allele	A/C
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:
2	chr6:27111921..27114869-chr6:27813562..27815611,2	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs149969	0.90[CEU][hapmap]
rs149970	0.90[CEU][hapmap]
rs200486	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs200502	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs200503	0.93[ASN][1000 genomes]
rs200504	0.87[ASN][1000 genomes]
rs200951	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs200956	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs200969	0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200978	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs200988	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs200991	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs201000	0.91[ASN][1000 genomes]
rs201001	0.91[ASN][1000 genomes]
rs201004	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2179095	0.84[CHD][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap]
rs510987	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs573179	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs742046	0.84[CHD][hapmap];0.89[LWK][hapmap]
rs7759217	0.84[CHD][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap]
rs9461405	0.84[CHD][hapmap];0.84[MEX][hapmap]

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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs200994	ZSCAN23	cis	cerebellum	SCAN
rs200994	HIST1H3C	cis	cerebellum	SCAN
rs200994	BTN3A3	cis	cerebellum	SCAN
rs200994	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs200994	HIST1H4J	cis	lymphoblastoid	seeQTL
rs200994	BTN3A2	cis	multi-tissue	Pritchard
rs200994	NKAPL	cis	parietal	SCAN
rs200994	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200994	LRRC16A	cis	parietal	SCAN
rs200994	AL022393.7	cis	Muscle Skeletal	GTEx
rs200994	ZKSCAN3	cis	parietal	SCAN
rs200994	ZNF192	cis	parietal	SCAN
rs200994	OR2B8P	cis	Thyroid	GTEx
rs200994	ZNF204P	cis	parietal	SCAN
rs200994	ZNF323	cis	cerebellum	SCAN
rs200994	BTN2A2	Cis_chr	lymphoblastoid	RTeQTL
rs200994	ZNF323	cis	parietal	SCAN
rs200994	BTN2A1	cis	parietal	SCAN
rs200994	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200994	ZNF187	cis	parietal	SCAN
rs200994	ZNF192	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27807600-27816600	Weak transcription	Pancreas	Pancrea
2	chr6:27807800-27814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:27808000-27815800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:27808000-27819000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:27808000-27822400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:27808000-27831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:27808200-27815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:27808200-27815200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:27808200-27817200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:27808200-27818800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:27808200-27830600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:27808400-27814400	Weak transcription	HepG2	liver
13	chr6:27808400-27814800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:27808400-27815000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:27808400-27815000	Weak transcription	NHDF-Ad	bronchial
16	chr6:27808400-27815600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:27808400-27818000	Weak transcription	Hela-S3	cervix
18	chr6:27810200-27814400	Weak transcription	A549	lung
19	chr6:27810200-27816800	Strong transcription	K562	blood
20	chr6:27810400-27817800	Weak transcription	Fetal Thymus	thymus
21	chr6:27813000-27814000	Strong transcription	GM12878-XiMat	blood
22	chr6:27813000-27814000	Strong transcription	HSMMtube	muscle
23	chr6:27813600-27815400	Weak transcription	Liver	Liver
24	chr6:27813800-27822200	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links