Variant report

Variant	rs12613488
Chromosome Location	chr2:15433328-15433329
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:15426134..15427751-chr2:15431518..15433743,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10167186	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10181295	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10193783	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10193872	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10199552	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10199885	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10206116	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1076509	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803672	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10929355	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10929356	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10929357	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11686627	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11892206	0.82[AMR][1000 genomes]
rs11904635	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692259	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12993581	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12993786	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1318102	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1808361	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1974772	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1989380	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2020147	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2042144	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755127	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805093	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805095	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3828463	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4465744	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668889	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668890	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668891	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668892	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4668893	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6431688	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6431689	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6431690	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6431691	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6708720	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711181	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6731789	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6732362	0.87[EUR][1000 genomes]
rs6738994	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746672	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756029	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs721858	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7340328	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs741570	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7575687	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7584861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7598652	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7599455	0.88[EUR][1000 genomes]
rs7605754	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs888636	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs929735	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs962616	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9711182	0.88[EUR][1000 genomes]
rs9917271	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[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	nsv515567	chr2:15004748-15906778	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv529077	chr2:15143950-15722947	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv948649	chr2:15273933-15572834	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2762245	chr2:15418054-15480441	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:15365000-15442400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:15371400-15468400	Weak transcription	Esophagus	oesophagus
3	chr2:15375000-15446000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:15375000-15469000	Weak transcription	Psoas Muscle	Psoas
5	chr2:15392400-15463400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:15399600-15453600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:15399800-15440600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:15399800-15470600	Weak transcription	HUVEC	blood vessel
9	chr2:15400600-15468400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:15400800-15456400	Weak transcription	Pancreas	Pancrea
11	chr2:15401200-15469600	Weak transcription	Small Intestine	intestine
12	chr2:15402400-15457000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:15406200-15438600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:15406200-15440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:15407400-15450000	Weak transcription	HMEC	breast
16	chr2:15411400-15433400	Strong transcription	Primary T cells from cord blood	blood
17	chr2:15412000-15437400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:15412000-15440800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:15413000-15440600	Weak transcription	NHLF	lung
20	chr2:15413800-15453600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:15415200-15437000	Weak transcription	Hela-S3	cervix
22	chr2:15416000-15437200	Weak transcription	A549	lung
23	chr2:15416000-15444400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:15416200-15439000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:15416200-15440800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:15416200-15478200	Weak transcription	NH-A	brain
27	chr2:15416600-15433400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:15420200-15436400	Strong transcription	Primary B cells from cord blood	blood
29	chr2:15421000-15494800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:15421200-15440400	Weak transcription	Fetal Heart	heart
31	chr2:15421200-15442400	Weak transcription	Gastric	stomach
32	chr2:15422200-15446400	Weak transcription	GM12878-XiMat	blood
33	chr2:15422400-15439800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:15422800-15439400	Strong transcription	Fetal Intestine Large	intestine
35	chr2:15423800-15438600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:15424200-15446600	Weak transcription	HSMM	muscle
37	chr2:15424400-15452000	Weak transcription	Stomach Mucosa	stomach
38	chr2:15424600-15442400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:15425000-15458000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:15425600-15442200	Weak transcription	Brain Germinal Matrix	brain
41	chr2:15426600-15433800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr2:15426800-15473200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:15426800-15520000	Weak transcription	Colonic Mucosa	Colon
44	chr2:15427400-15437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:15427400-15443200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:15427400-15451400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:15427400-15453400	Weak transcription	Fetal Brain Female	brain
48	chr2:15427400-15456600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:15427400-15467800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:15427400-15470200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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