Variant report

Variant	rs1838967
Chromosome Location	chr6:25134658-25134659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1547054	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1823184	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923195	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2145769	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2295737	0.80[ASN][1000 genomes]
rs2516577	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2894033	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs302967	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs303022	0.80[ASN][1000 genomes]
rs303023	0.80[ASN][1000 genomes]
rs303025	0.80[ASN][1000 genomes]
rs3812105	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4712887	0.80[ASN][1000 genomes]
rs6919920	0.80[ASN][1000 genomes]
rs7740661	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7740668	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7773802	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7775959	0.81[AMR][1000 genomes]
rs7776121	0.81[AMR][1000 genomes]
rs9379721	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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
rs1838967	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
2	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:25113000-25136800	Weak transcription	Osteobl	bone
4	chr6:25116000-25137000	Weak transcription	Lung	lung
5	chr6:25122600-25137000	Weak transcription	Colonic Mucosa	Colon
6	chr6:25122600-25137000	Weak transcription	HSMM	muscle
7	chr6:25122800-25137000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:25123600-25136600	Weak transcription	HSMMtube	muscle
9	chr6:25123800-25136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
11	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
12	chr6:25126200-25136400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:25126400-25135400	Weak transcription	Thymus	Thymus
14	chr6:25126400-25136800	Weak transcription	Liver	Liver
15	chr6:25128200-25135000	Weak transcription	Placenta	Placenta
16	chr6:25128400-25135200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:25129400-25136400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:25129600-25136800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:25129800-25135400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:25130600-25136800	Weak transcription	Ovary	ovary
21	chr6:25131000-25134800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:25131800-25136600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr6:25132000-25136600	ZNF genes & repeats	Dnd41	blood
24	chr6:25132200-25136000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr6:25132400-25134800	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:25132400-25136800	Weak transcription	Adipose Nuclei	Adipose
27	chr6:25132800-25136600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr6:25133000-25135400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:25133000-25135800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:25133200-25135600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr6:25133200-25137000	Strong transcription	Fetal Thymus	thymus
32	chr6:25133400-25135600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:25133800-25136000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:25133800-25136200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr6:25133800-25138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:25134000-25134800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:25134000-25135200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:25134000-25136200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:25134000-25136200	Weak transcription	Aorta	Aorta
40	chr6:25134000-25136200	Weak transcription	Left Ventricle	heart
41	chr6:25134000-25136800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:25134000-25137200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:25134200-25134800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr6:25134200-25135200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:25134200-25135200	Weak transcription	Right Atrium	heart
46	chr6:25134200-25135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:25134200-25135400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:25134200-25135800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:25134200-25136000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:25134200-25136200	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links