Variant report

Variant	rs1377946
Chromosome Location	chr2:33439121-33439122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10205739	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10211514	0.81[ASN][1000 genomes]
rs10432657	0.81[CEU][hapmap]
rs10495783	1.00[CEU][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10495784	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124309	0.89[CEU][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs11124310	0.81[ASN][1000 genomes]
rs11681694	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12611532	0.84[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13021881	0.89[ASN][1000 genomes]
rs1377945	0.81[JPT][hapmap]
rs1377947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1454376	0.94[ASN][1000 genomes]
rs1454378	0.85[ASN][1000 genomes]
rs1454379	0.94[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17567417	0.84[CHD][hapmap]
rs17568051	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17640469	0.96[CEU][hapmap]
rs17641115	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17641180	0.80[CHB][hapmap]
rs17641906	0.80[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs17642074	0.80[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs1869542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2061026	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2061027	0.80[CHB][hapmap]
rs2290448	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2290449	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2367619	0.82[ASN][1000 genomes]
rs2367623	0.80[CHB][hapmap];0.86[CHD][hapmap]
rs2367624	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4542826	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4670184	0.82[EUR][1000 genomes]
rs4670225	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4670252	0.82[ASN][1000 genomes]
rs4670307	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670313	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670822	0.82[ASN][1000 genomes]
rs4670833	0.82[ASN][1000 genomes]
rs4670857	0.81[CEU][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4670860	0.85[CEU][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4670863	0.82[ASN][1000 genomes]
rs4671010	0.80[CHB][hapmap]
rs4671016	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671024	0.81[ASN][1000 genomes]
rs4671035	0.80[CHB][hapmap]
rs5006124	0.82[ASN][1000 genomes]
rs5006125	0.83[ASN][1000 genomes]
rs55957962	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56163907	0.82[ASN][1000 genomes]
rs58920936	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62146704	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62146732	0.81[ASN][1000 genomes]
rs6543691	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6543698	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs6543700	0.83[CEU][hapmap]
rs6707911	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707962	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6708836	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6712473	0.85[CEU][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6720059	0.81[ASN][1000 genomes]
rs6720185	0.85[CEU][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs6726760	0.89[ASN][1000 genomes]
rs6728094	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs6736908	0.83[ASN][1000 genomes]
rs6743685	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs6751657	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6759943	0.81[ASN][1000 genomes]
rs7423390	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7571401	0.92[CEU][hapmap]
rs7580348	0.80[CHB][hapmap]
rs7608222	0.81[ASN][1000 genomes]
rs7608535	0.81[ASN][1000 genomes]
rs9308931	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs961239	0.92[CEU][hapmap]
rs964702	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs996102	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs996103	0.80[CHB][hapmap];0.86[CHD][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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33409200-33441600	Weak transcription	Psoas Muscle	Psoas
3	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
4	chr2:33415200-33441600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:33415400-33441600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:33423000-33439400	Weak transcription	Pancreas	Pancrea
7	chr2:33423000-33439600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:33428600-33439200	Weak transcription	Right Atrium	heart
9	chr2:33434200-33439400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:33434200-33442200	Enhancers	HUVEC	blood vessel
11	chr2:33434600-33439400	Weak transcription	Lung	lung
12	chr2:33434600-33439400	Weak transcription	Right Ventricle	heart
13	chr2:33435000-33439400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:33435800-33444400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:33436000-33439400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:33436000-33441000	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:33436200-33440000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:33436400-33439600	Enhancers	Aorta	Aorta
19	chr2:33436400-33439800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:33436400-33442200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:33436600-33440200	Weak transcription	HSMM	muscle
22	chr2:33436600-33441600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:33436600-33444200	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:33436800-33439200	Weak transcription	Left Ventricle	heart
25	chr2:33436800-33440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:33436800-33440400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:33436800-33443800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:33436800-33455000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:33437200-33443400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:33437400-33439200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:33437400-33439400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:33437400-33444200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:33437600-33439400	Weak transcription	NHEK	skin
34	chr2:33437600-33441200	Weak transcription	HSMMtube	muscle
35	chr2:33437600-33441600	Weak transcription	Liver	Liver
36	chr2:33437800-33439200	Weak transcription	Stomach Mucosa	stomach
37	chr2:33437800-33439400	Weak transcription	HMEC	breast
38	chr2:33437800-33439800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:33437800-33440000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:33437800-33442200	Enhancers	NH-A	brain
41	chr2:33437800-33444400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:33437800-33444600	Weak transcription	Hela-S3	cervix
43	chr2:33437800-33445200	Weak transcription	Fetal Kidney	kidney
44	chr2:33438000-33440000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:33438000-33443000	Enhancers	A549	lung
46	chr2:33438200-33439200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:33438200-33439400	Weak transcription	Ovary	ovary
48	chr2:33438200-33439600	Weak transcription	K562	blood
49	chr2:33438200-33441600	Weak transcription	Esophagus	oesophagus
50	chr2:33438600-33440400	Enhancers	Rectal Smooth Muscle	rectum

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