Variant report

Variant	rs303005
Chromosome Location	chr6:25086644-25086645
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	chr6:25085087..25087243-chr6:25089273..25091853,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1665820	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810471	1.00[CHB][hapmap]
rs182499	0.86[ASN][1000 genomes]
rs188567	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2690056	1.00[CHB][hapmap]
rs2690062	1.00[CHB][hapmap]
rs2690066	1.00[CHB][hapmap]
rs2744263	1.00[CHB][hapmap]
rs2744273	1.00[CHB][hapmap]
rs2744274	1.00[CHB][hapmap]
rs2744279	1.00[CHB][hapmap]
rs2744281	1.00[CHB][hapmap]
rs2744286	1.00[CHB][hapmap]
rs302981	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs302985	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303001	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303002	1.00[ASN][1000 genomes]
rs303003	0.86[ASN][1000 genomes]
rs303010	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303011	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303012	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs416030	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4594940	1.00[CHB][hapmap]
rs6456661	1.00[CHB][hapmap]
rs7740534	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743508	1.00[CHB][hapmap]
rs7743997	1.00[CHB][hapmap]
rs9461103	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs303005	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25079400-25093000	Weak transcription	Ovary	ovary
2	chr6:25079600-25086800	Weak transcription	Aorta	Aorta
3	chr6:25079800-25086800	Weak transcription	Spleen	Spleen
4	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:25081600-25088800	Weak transcription	Osteobl	bone
7	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:25083000-25086800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:25083800-25089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
12	chr6:25084000-25087600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:25084200-25087000	Enhancers	Liver	Liver
14	chr6:25084200-25089800	Weak transcription	Hela-S3	cervix
15	chr6:25084800-25086800	Weak transcription	Left Ventricle	heart
16	chr6:25084800-25088400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
18	chr6:25084800-25113800	Weak transcription	Gastric	stomach
19	chr6:25085000-25086800	Weak transcription	HSMMtube	muscle
20	chr6:25085000-25087000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:25085000-25088600	Weak transcription	Lung	lung
22	chr6:25085000-25088600	Enhancers	HUVEC	blood vessel
23	chr6:25085200-25086800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:25085200-25086800	Weak transcription	Small Intestine	intestine
25	chr6:25085200-25087600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:25085200-25087600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr6:25085200-25088000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:25085200-25089400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:25085400-25087200	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:25085400-25088200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:25085600-25086800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:25085600-25087400	Enhancers	Primary B cells from cord blood	blood
35	chr6:25085600-25087800	Enhancers	Primary B cells from peripheral blood	blood
36	chr6:25085600-25088000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr6:25085800-25086800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr6:25085800-25087000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:25085800-25087400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:25085800-25088400	Genic enhancers	Dnd41	blood
41	chr6:25086000-25087000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr6:25086000-25087000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr6:25086000-25087000	Enhancers	GM12878-XiMat	blood
44	chr6:25086000-25087200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr6:25086000-25087200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr6:25086200-25087200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr6:25086200-25087200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:25086200-25087800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:25086200-25088600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:25086200-25096400	Strong transcription	Thymus	Thymus

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