Variant report

Variant	rs17562423
Chromosome Location	chr2:64200119-64200120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64198229..64200960-chr2:64202925..64205007,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10183479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs10650017	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11558741	0.90[ASN][1000 genomes]
rs11674020	0.88[ASN][1000 genomes]
rs11676710	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11682249	1.00[YRI][hapmap]
rs11683408	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11691987	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs11693906	0.81[ASN][1000 genomes]
rs12713498	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12996866	0.90[ASN][1000 genomes]
rs13018690	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs13431781	0.90[ASN][1000 genomes]
rs1440002	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17562177	0.88[ASN][1000 genomes]
rs193031	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2302808	0.88[ASN][1000 genomes]
rs2439183	0.94[ASN][1000 genomes]
rs2969395	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs329478	0.98[ASN][1000 genomes]
rs329488	0.89[ASN][1000 genomes]
rs34122334	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34765999	0.98[ASN][1000 genomes]
rs34777730	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[ASN][1000 genomes]
rs35002211	0.88[ASN][1000 genomes]
rs35336851	0.93[ASN][1000 genomes]
rs35480874	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35697586	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35960986	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs36033991	0.88[ASN][1000 genomes]
rs36123537	0.96[ASN][1000 genomes]
rs4233930	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4538187	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs4671071	0.85[ASN][1000 genomes]
rs4671073	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56904032	0.98[ASN][1000 genomes]
rs6546029	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6546030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6546032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6546033	0.88[ASN][1000 genomes]
rs6546035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs66980330	0.90[ASN][1000 genomes]
rs6710763	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs67308158	0.90[ASN][1000 genomes]
rs6731508	0.90[ASN][1000 genomes]
rs6732746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs6755646	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs67615384	0.90[ASN][1000 genomes]
rs67765474	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs68117986	0.98[ASN][1000 genomes]
rs72808243	0.86[ASN][1000 genomes]
rs72893103	0.98[ASN][1000 genomes]
rs74181291	0.88[ASN][1000 genomes]
rs7590399	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002209	chr2:64160385-64238475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64114000-64212000	Weak transcription	Small Intestine	intestine
2	chr2:64129600-64201000	Weak transcription	Hela-S3	cervix
3	chr2:64130400-64211200	Weak transcription	Fetal Brain Male	brain
4	chr2:64137400-64204800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:64139800-64220600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:64154400-64202600	Weak transcription	Spleen	Spleen
7	chr2:64154600-64202600	Weak transcription	Pancreas	Pancrea
8	chr2:64154800-64242600	Weak transcription	Aorta	Aorta
9	chr2:64159600-64211600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:64163200-64207600	Weak transcription	HUVEC	blood vessel
11	chr2:64165800-64202600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:64166800-64202600	Weak transcription	HMEC	breast
13	chr2:64168600-64202600	Weak transcription	Esophagus	oesophagus
14	chr2:64168600-64202600	Weak transcription	K562	blood
15	chr2:64168800-64204800	Weak transcription	Psoas Muscle	Psoas
16	chr2:64169000-64215000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:64173600-64202800	Weak transcription	Fetal Brain Female	brain
18	chr2:64175200-64203000	Weak transcription	Thymus	Thymus
19	chr2:64175600-64213000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:64175800-64202800	Weak transcription	Gastric	stomach
21	chr2:64176000-64202600	Weak transcription	Lung	lung
22	chr2:64176000-64204600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:64176000-64228000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:64176200-64205400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:64176400-64205000	Weak transcription	Brain Germinal Matrix	brain
26	chr2:64177600-64200800	Weak transcription	Fetal Kidney	kidney
27	chr2:64177600-64204600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:64177600-64212600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:64178200-64211400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:64178800-64202200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:64178800-64202600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:64179200-64202600	Weak transcription	Ovary	ovary
33	chr2:64183800-64204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:64184000-64205200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr2:64185600-64203800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:64185800-64245000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:64186800-64216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:64187600-64201800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:64187600-64202800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:64187600-64203200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:64187600-64210200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:64187600-64211400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:64187800-64210200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:64187800-64211200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:64188000-64210000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:64189600-64204800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:64189800-64204800	Weak transcription	A549	lung
48	chr2:64189800-64205000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:64190000-64203000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:64190000-64205200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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