Variant report

Variant	rs892464
Chromosome Location	chr2:110343913-110343914
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11541143	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1560884	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1808722	0.86[EUR][1000 genomes]
rs2018352	0.81[ASN][1000 genomes]
rs2043462	0.87[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs2060403	0.87[CHB][hapmap]
rs28369323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28588372	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28624186	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2867277	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28853417	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs4953760	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs4953784	0.87[CHB][hapmap]
rs4953843	0.82[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs58012425	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61215808	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61548546	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6594037	0.87[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs6594041	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6705503	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6716287	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6723295	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs6735752	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs6752531	0.83[EUR][1000 genomes]
rs6760478	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs717189	0.83[EUR][1000 genomes]
rs72938271	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747445	0.80[ASN][1000 genomes]
rs7572991	0.91[MKK][hapmap]
rs7579996	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7596172	0.81[ASN][1000 genomes]
rs767628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892460	0.81[ASN][1000 genomes]
rs919941	0.82[CHB][hapmap]
rs9330316	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9751601	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110352200	Weak transcription	Gastric	stomach
2	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
3	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
6	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
8	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
9	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
11	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
15	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:110323400-110348000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:110323400-110348200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:110323600-110344200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:110324000-110348400	Weak transcription	Hela-S3	cervix
21	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
22	chr2:110324200-110348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:110328800-110349000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:110329000-110369000	Weak transcription	Ovary	ovary
26	chr2:110329200-110359400	Weak transcription	NHLF	lung
27	chr2:110329200-110369400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:110329400-110359600	Weak transcription	NHDF-Ad	bronchial
29	chr2:110329600-110351200	Weak transcription	HMEC	breast
30	chr2:110329600-110351600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:110329800-110351600	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:110332000-110348200	Weak transcription	Right Ventricle	heart
33	chr2:110332200-110352600	Weak transcription	Fetal Lung	lung
34	chr2:110333800-110344400	Weak transcription	Liver	Liver
35	chr2:110335600-110346600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:110336600-110348600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:110337600-110344400	Strong transcription	HepG2	liver
38	chr2:110338600-110354600	Weak transcription	Right Atrium	heart
39	chr2:110338600-110357600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:110338800-110348200	Weak transcription	Lung	lung
41	chr2:110338800-110352600	Weak transcription	Fetal Intestine Large	intestine
42	chr2:110339000-110346600	Weak transcription	Fetal Stomach	stomach
43	chr2:110340200-110346600	Weak transcription	Fetal Intestine Small	intestine
44	chr2:110340600-110344000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:110341000-110351600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:110341200-110344000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:110341400-110344000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:110341400-110344000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:110341600-110344000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:110341600-110349200	Weak transcription	Fetal Muscle Trunk	muscle

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