Variant report

Variant	rs13425449
Chromosome Location	chr2:54382613-54382614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10173565	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10186140	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10201710	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206954	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11125522	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11689599	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11884229	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11884435	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12615044	0.89[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12617094	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12620359	0.84[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13399590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13406537	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13412967	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13417064	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1421618	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1421619	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17045536	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2112126	0.81[ASN][1000 genomes]
rs2112127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287640	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2287641	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2287644	0.81[ASN][1000 genomes]
rs2287645	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs3738854	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes]
rs3738855	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3929001	0.84[CHB][hapmap]
rs55762565	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55994902	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56696975	0.92[ASN][1000 genomes]
rs57437150	0.94[ASN][1000 genomes]
rs57536238	0.94[ASN][1000 genomes]
rs57940005	0.81[ASN][1000 genomes]
rs57940820	0.81[ASN][1000 genomes]
rs57995357	0.90[ASN][1000 genomes]
rs59397800	0.88[AMR][1000 genomes]
rs59495263	0.95[ASN][1000 genomes]
rs59749650	0.81[ASN][1000 genomes]
rs59929874	0.95[ASN][1000 genomes]
rs59936071	0.95[ASN][1000 genomes]
rs60798176	0.90[ASN][1000 genomes]
rs61434527	0.95[ASN][1000 genomes]
rs6545387	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713993	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6742463	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72800778	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7558563	0.81[ASN][1000 genomes]
rs7572559	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7574376	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7593897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9631060	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs977784	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
9	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	nsv1006984	chr2:54343466-54384094	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv874148	chr2:54344325-54432222	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1003889	chr2:54347750-54424601	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv582011	chr2:54348704-54384927	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1011433	chr2:54351145-54424601	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1012230	chr2:54351988-54422959	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv874149	chr2:54358517-54432222	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54343400-54388600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:54352200-54411400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:54361400-54389800	Weak transcription	Lung	lung
4	chr2:54362000-54386800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:54362000-54416400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr2:54362200-54391400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:54362200-54411200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:54362400-54386800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:54362800-54387000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:54366400-54389200	Weak transcription	Fetal Stomach	stomach
11	chr2:54366400-54391200	Weak transcription	Spleen	Spleen
12	chr2:54366400-54397200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:54366600-54409600	Weak transcription	Psoas Muscle	Psoas
14	chr2:54367400-54416600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:54368000-54383800	Weak transcription	Gastric	stomach
16	chr2:54369600-54416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:54371400-54387000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:54377400-54391200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:54377600-54386800	Weak transcription	Adipose Nuclei	Adipose
20	chr2:54377800-54382800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:54377800-54387000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:54377800-54387000	Weak transcription	HSMMtube	muscle
23	chr2:54379800-54383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:54380400-54386800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:54380600-54429200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:54380600-54434400	Weak transcription	Ovary	ovary
27	chr2:54380800-54387000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:54382200-54389200	Weak transcription	Fetal Heart	heart
29	chr2:54382400-54382800	ZNF genes & repeats	Brain Anterior Caudate	brain
30	chr2:54382400-54382800	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr2:54382400-54383000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr2:54382400-54383000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:54382400-54383000	Strong transcription	Brain Hippocampus Middle	brain
34	chr2:54382400-54383000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:54382400-54383000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr2:54382400-54383400	Strong transcription	Liver	Liver
37	chr2:54382400-54383800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr2:54382600-54382800	ZNF genes & repeats	Aorta	Aorta
39	chr2:54382600-54382800	ZNF genes & repeats	Esophagus	oesophagus
40	chr2:54382600-54382800	ZNF genes & repeats	Fetal Brain Male	brain
41	chr2:54382600-54382800	ZNF genes & repeats	Fetal Lung	lung
42	chr2:54382600-54382800	ZNF genes & repeats	Left Ventricle	heart
43	chr2:54382600-54382800	ZNF genes & repeats	Pancreas	Pancrea
44	chr2:54382600-54382800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr2:54382600-54382800	ZNF genes & repeats	Right Ventricle	heart
46	chr2:54382600-54382800	ZNF genes & repeats	NHDF-Ad	bronchial
47	chr2:54382600-54383000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:54382600-54383000	ZNF genes & repeats	Primary B cells from cord blood	blood
49	chr2:54382600-54383000	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr2:54382600-54383000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain

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