Variant report

Variant	rs10176828
Chromosome Location	chr2:180044186-180044187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10172589	1.00[ASN][1000 genomes]
rs10173853	1.00[AMR][1000 genomes]
rs10178559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10186707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10207754	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10208882	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10209875	1.00[CHB][hapmap]
rs10221811	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12328593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12329222	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12611473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12612427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12613089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12616452	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12617364	1.00[AMR][1000 genomes]
rs12618724	0.85[ASN][1000 genomes]
rs12622434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13382573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13383806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13387502	0.85[ASN][1000 genomes]
rs13391187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13394908	1.00[AMR][1000 genomes]
rs13395559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13408774	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13412820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13417112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13422693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13424092	1.00[CHB][hapmap]
rs13429191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16866630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28362046	0.90[ASN][1000 genomes]
rs28508327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35041512	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734127	1.00[AMR][1000 genomes]
rs7578417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7581898	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7588135	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7601965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7608106	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9288024	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
3	chr2:179980000-180056800	Weak transcription	HSMM	muscle
4	chr2:179996200-180047600	Weak transcription	NH-A	brain
5	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
6	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
7	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
9	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
10	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
11	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
12	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
14	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
15	chr2:180015000-180054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:180015000-180060600	Weak transcription	Lung	lung
18	chr2:180015200-180046200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:180015200-180047200	Weak transcription	Placenta	Placenta
20	chr2:180015400-180046000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:180015400-180049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:180015400-180058000	Weak transcription	Fetal Stomach	stomach
23	chr2:180015400-180060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:180016000-180049000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:180016000-180054200	Weak transcription	NHDF-Ad	bronchial
26	chr2:180016200-180054000	Weak transcription	Osteobl	bone
27	chr2:180023000-180052800	Weak transcription	Fetal Heart	heart
28	chr2:180024200-180045800	Weak transcription	GM12878-XiMat	blood
29	chr2:180024400-180048600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:180026400-180048800	Weak transcription	Fetal Intestine Small	intestine
31	chr2:180030400-180055400	Weak transcription	Thymus	Thymus
32	chr2:180030800-180046000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:180030800-180050800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:180031200-180052000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:180031400-180050000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:180031800-180045600	Weak transcription	Fetal Brain Female	brain
37	chr2:180032000-180045000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:180032200-180050800	Weak transcription	NHEK	skin
39	chr2:180032200-180067600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:180033000-180047800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:180033000-180049600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:180033200-180044800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:180036200-180048000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:180036600-180051800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:180036600-180053200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:180037400-180045600	Strong transcription	Primary B cells from cord blood	blood
47	chr2:180037600-180045400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:180037600-180047800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:180037600-180058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:180038000-180045800	Weak transcription	H1 Cell Line	embryonic stem cell

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