Variant report

Variant	rs17023600
Chromosome Location	chr2:39516309-39516310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10199459	0.94[EUR][1000 genomes]
rs11124683	0.89[EUR][1000 genomes]
rs11884949	0.81[ASN][1000 genomes]
rs11896389	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12328714	0.88[EUR][1000 genomes]
rs17023530	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17023542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023611	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17023640	1.00[CHB][hapmap]
rs17023684	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023696	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023773	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17446102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17446515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17446690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17505580	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17505877	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056653	0.94[EUR][1000 genomes]
rs2056655	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs2111383	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2373532	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs3732052	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4670273	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs4670938	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4670940	0.82[JPT][hapmap]
rs55761128	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56287463	0.91[AFR][1000 genomes]
rs6544227	0.91[EUR][1000 genomes]
rs6544229	0.94[EUR][1000 genomes]
rs6720537	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs6720951	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs6721740	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6758596	0.82[CEU][hapmap];0.94[EUR][1000 genomes]
rs73924009	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7559436	0.94[EUR][1000 genomes]
rs7577097	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7605939	0.82[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription 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	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS 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	21 gene(s)	inside rSNPs	diseases
14	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv873886	chr2:39468676-39573521	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	esv1809158	chr2:39474679-39588797	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv1828851	chr2:39508121-39588797	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv873888	chr2:39508830-39573521	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
4	chr2:39479000-39521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:39481000-39580200	Weak transcription	NHEK	skin
6	chr2:39484400-39516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:39493600-39523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:39493800-39516600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:39493800-39525000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:39494000-39525600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
13	chr2:39495600-39523200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:39496400-39521200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:39496600-39520400	Strong transcription	Placenta	Placenta
16	chr2:39497000-39516600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:39504400-39521400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:39504600-39523600	Weak transcription	Brain Substantia Nigra	brain
19	chr2:39504600-39540000	Weak transcription	Right Ventricle	heart
20	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
21	chr2:39504800-39518400	Weak transcription	Esophagus	oesophagus
22	chr2:39504800-39518800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:39504800-39521800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:39504800-39527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:39504800-39538400	Weak transcription	Small Intestine	intestine
26	chr2:39504800-39541600	Weak transcription	Fetal Brain Male	brain
27	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
29	chr2:39505000-39518600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:39505000-39523400	Weak transcription	Brain Germinal Matrix	brain
31	chr2:39505000-39527400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:39505000-39538200	Weak transcription	Lung	lung
33	chr2:39505200-39518400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:39505400-39517600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:39505400-39518000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:39505400-39519400	Weak transcription	Spleen	Spleen
37	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
38	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:39505600-39540000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:39506000-39518800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:39507000-39517800	Weak transcription	Fetal Thymus	thymus
43	chr2:39507200-39538400	Weak transcription	Aorta	Aorta
44	chr2:39507600-39522200	Strong transcription	HSMM	muscle
45	chr2:39508000-39521000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:39508600-39520000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:39508600-39521800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:39508800-39527400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:39509000-39521800	Strong transcription	HepG2	liver
50	chr2:39509200-39521800	Strong transcription	Liver	Liver

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