Variant report

Variant	rs2331626
Chromosome Location	chr1:180632617-180632618
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10914061	0.91[ASN][1000 genomes]
rs10914096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12085097	0.86[EUR][1000 genomes]
rs12118646	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1339768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1970404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2331886	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2944259	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2944262	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002113	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3002115	0.88[EUR][1000 genomes]
rs3002116	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3013633	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3013634	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3789366	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3843278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3845406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3856058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3897798	0.88[ASN][1000 genomes]
rs4083591	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4108558	0.95[EUR][1000 genomes]
rs4651073	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs66520411	0.88[EUR][1000 genomes]
rs6659049	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659368	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661105	0.91[CHB][hapmap]
rs6682974	0.87[EUR][1000 genomes]
rs67780680	0.93[EUR][1000 genomes]
rs72707408	0.84[EUR][1000 genomes]
rs72723045	0.88[EUR][1000 genomes]
rs7514404	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7524547	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541650	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs7548318	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7550031	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9425881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9970145	0.91[CHB][hapmap]
rs9970363	0.82[CHB][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv988017	chr1:180630648-180639452	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180645200	Weak transcription	Gastric	stomach
2	chr1:180619600-180634600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:180625800-180634800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:180627600-180632800	Weak transcription	A549	lung
5	chr1:180627600-180640000	Weak transcription	Fetal Heart	heart
6	chr1:180627800-180634200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:180629200-180633800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:180629600-180641000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:180630800-180634400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:180631000-180633600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:180631000-180634200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:180631200-180635000	Weak transcription	HMEC	breast
13	chr1:180631200-180636000	Weak transcription	Ovary	ovary
14	chr1:180631400-180635000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:180631600-180644400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:180631800-180633400	Weak transcription	Left Ventricle	heart
17	chr1:180631800-180635000	ZNF genes & repeats	Fetal Brain Female	brain
18	chr1:180632000-180632800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr1:180632000-180633000	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr1:180632200-180633000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
21	chr1:180632200-180635000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:180632200-180635000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
23	chr1:180632200-180644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:180632400-180633600	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr1:180632400-180633800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:180632400-180634600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:180632400-180634800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:180632400-180634800	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr1:180632400-180634800	Strong transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:180632400-180635000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:180632400-180635400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:180632400-180635400	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr1:180632600-180633000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:180632600-180633000	Strong transcription	Pancreas	Pancrea
35	chr1:180632600-180633200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:180632600-180633600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:180632600-180633800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:180632600-180633800	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr1:180632600-180634400	Strong transcription	Aorta	Aorta
40	chr1:180632600-180634800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:180632600-180635000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood

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