Variant report

Variant	rs17045242
Chromosome Location	chr2:54033463-54033464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10180492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188834	1.00[ASN][1000 genomes]
rs10199444	1.00[ASN][1000 genomes]
rs10199995	1.00[ASN][1000 genomes]
rs10205469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10208649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10209918	1.00[ASN][1000 genomes]
rs1049894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125517	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886024	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11890472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11891000	1.00[ASN][1000 genomes]
rs11892759	1.00[ASN][1000 genomes]
rs11894028	1.00[ASN][1000 genomes]
rs11904365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13382257	1.00[ASN][1000 genomes]
rs13387291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389673	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13402778	1.00[ASN][1000 genomes]
rs13408425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13417051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13432387	1.00[ASN][1000 genomes]
rs1404994	1.00[ASN][1000 genomes]
rs2177791	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177792	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287347	0.80[CEU][hapmap]
rs28391754	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28699646	0.88[EUR][1000 genomes]
rs3930909	1.00[ASN][1000 genomes]
rs41536750	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59172147	0.88[EUR][1000 genomes]
rs60769690	1.00[ASN][1000 genomes]
rs6545367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545368	0.80[CEU][hapmap]
rs6545369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545372	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712561	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6723722	1.00[ASN][1000 genomes]
rs6731217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731911	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740063	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745729	1.00[ASN][1000 genomes]
rs6751340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6756424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6759437	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760038	1.00[ASN][1000 genomes]
rs6761648	1.00[ASN][1000 genomes]
rs724387	1.00[ASN][1000 genomes]
rs72902931	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937421	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7560575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565152	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567225	1.00[ASN][1000 genomes]
rs7594327	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599335	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608085	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608989	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309251	0.81[EUR][1000 genomes];1.00[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
2	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
4	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
5	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:54015800-54038400	Weak transcription	Fetal Heart	heart
10	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:54016400-54043000	Weak transcription	Gastric	stomach
12	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
13	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:54020600-54048600	Strong transcription	Osteobl	bone
16	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
21	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
24	chr2:54021600-54035000	Strong transcription	Liver	Liver
25	chr2:54021600-54046400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:54022000-54039400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:54022000-54044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:54022000-54047000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:54022000-54047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:54022200-54039000	Strong transcription	Fetal Intestine Large	intestine
34	chr2:54022200-54046200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr2:54022200-54046600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:54022200-54047200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:54024200-54043400	Strong transcription	Dnd41	blood
39	chr2:54024400-54035000	Weak transcription	HSMMtube	muscle
40	chr2:54024800-54039600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:54024800-54045400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:54025000-54040000	Weak transcription	K562	blood
43	chr2:54025800-54035400	Weak transcription	Pancreas	Pancrea
44	chr2:54025800-54036600	Weak transcription	Spleen	Spleen
45	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
46	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:54026400-54033600	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:54026400-54034000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:54026600-54035800	Weak transcription	Brain Anterior Caudate	brain
50	chr2:54026600-54038000	Weak transcription	Fetal Brain Male	brain

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