Variant report

Variant	rs516361
Chromosome Location	chr6:25052029-25052030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs177356	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186237	0.87[CHD][hapmap]
rs303878	0.83[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs304256	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304257	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304258	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304259	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458664	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466882	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466944	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513585	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549256	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550176	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609408	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv10579	chr6:25045015-25053354	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs516361	HIST1H2AA	cis	parietal	SCAN
rs516361	CMAH	cis	lymphoblastoid	seeQTL
rs516361	CMAH	cis	parietal	SCAN
rs516361	CMAH	cis	cerebellum	SCAN
rs516361	HIST1H2AG	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25043200-25053400	Weak transcription	Spleen	Spleen
2	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:25049600-25058200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:25049600-25059200	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:25049800-25056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:25049800-25056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:25050000-25052200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:25050000-25052800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr6:25050000-25052800	Enhancers	Dnd41	blood
10	chr6:25050000-25056200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr6:25050200-25052400	Enhancers	Primary B cells from cord blood	blood
12	chr6:25050200-25052600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:25050200-25052800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:25050200-25053000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:25050200-25057800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:25050200-25058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:25050200-25058200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr6:25050400-25052400	Enhancers	GM12878-XiMat	blood
19	chr6:25050400-25054400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr6:25050400-25054600	Enhancers	NHDF-Ad	bronchial
21	chr6:25050400-25056000	Weak transcription	Thymus	Thymus
22	chr6:25050600-25055400	Enhancers	Placenta	Placenta
23	chr6:25050600-25059200	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:25050800-25054200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:25051000-25052200	Weak transcription	NHLF	lung
26	chr6:25051000-25052600	Enhancers	Stomach Mucosa	stomach
27	chr6:25051000-25053400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:25051000-25054000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:25051000-25054200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:25051000-25054400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:25051200-25053600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:25051200-25054000	Weak transcription	HSMM	muscle
33	chr6:25051200-25055000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:25051200-25056000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:25051200-25056200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:25051200-25061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25051400-25053200	Weak transcription	Fetal Thymus	thymus
38	chr6:25051400-25054200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:25051400-25056000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr6:25051400-25056200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:25051600-25053600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:25051600-25053800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:25051600-25054200	Weak transcription	HUVEC	blood vessel
44	chr6:25051600-25056000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:25051600-25056000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:25051800-25052600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:25051800-25053600	Weak transcription	Osteobl	bone
48	chr6:25051800-25053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:25051800-25054000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:25051800-25054000	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links