Variant report

Variant	rs12990262
Chromosome Location	chr2:148737829-148737830
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148736461..148738004-chr2:148741042..148743532,2	K562	blood:
2	chr2:148732231..148734888-chr2:148736487..148738854,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1014064	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1015096	0.81[ASN][1000 genomes]
rs1020653	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1030317	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10460259	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10497024	0.88[EUR][1000 genomes]
rs10803523	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1128919	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11888152	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11889608	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11901963	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904758	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12053113	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12053401	0.85[ASN][1000 genomes]
rs12104822	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12463798	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12464617	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12469015	0.93[EUR][1000 genomes]
rs12469939	0.95[EUR][1000 genomes]
rs12987286	0.88[EUR][1000 genomes]
rs12989596	0.80[EUR][1000 genomes]
rs12990959	0.81[EUR][1000 genomes]
rs12997165	0.83[ASN][1000 genomes]
rs12998729	0.87[EUR][1000 genomes]
rs13000597	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13004041	0.95[EUR][1000 genomes]
rs13004451	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006184	0.95[EUR][1000 genomes]
rs13007770	0.81[ASN][1000 genomes]
rs13008497	0.88[EUR][1000 genomes]
rs13008838	0.85[ASN][1000 genomes]
rs13012311	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13013743	0.84[EUR][1000 genomes]
rs13013867	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13014904	0.80[EUR][1000 genomes]
rs13014936	0.85[ASN][1000 genomes]
rs13017754	0.84[EUR][1000 genomes]
rs13019809	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13022962	0.85[ASN][1000 genomes]
rs13025219	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13025589	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13026220	0.84[EUR][1000 genomes]
rs13026650	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13027200	0.95[EUR][1000 genomes]
rs13027706	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028348	0.85[ASN][1000 genomes]
rs13028411	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13031064	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13032810	0.83[ASN][1000 genomes]
rs13033589	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13033696	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13034494	0.87[EUR][1000 genomes]
rs13034793	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13035475	0.85[ASN][1000 genomes]
rs1345994	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1364658	0.85[EUR][1000 genomes]
rs1424944	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1424954	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1469210	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1531032	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1895693	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2059422	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2161983	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2168145	0.82[ASN][1000 genomes]
rs2288190	0.83[ASN][1000 genomes]
rs2303392	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2307394	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34539489	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3764955	0.89[EUR][1000 genomes]
rs3768687	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3768689	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4972317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972318	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972356	0.84[EUR][1000 genomes]
rs4972357	0.83[EUR][1000 genomes]
rs57679331	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6430282	0.81[ASN][1000 genomes]
rs6711673	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6729465	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6729997	0.89[EUR][1000 genomes]
rs6760703	0.82[EUR][1000 genomes]
rs723681	0.89[EUR][1000 genomes]
rs7423878	0.87[AMR][1000 genomes]
rs7559714	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7559925	0.87[EUR][1000 genomes]
rs7594075	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929939	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9789434	0.86[ASN][1000 genomes]
rs9789640	0.81[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	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1004169	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv535970	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1009807	chr2:148731025-148829378	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv535973	chr2:148731025-148829378	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148658800-148741600	Weak transcription	Aorta	Aorta
3	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:148694400-148738400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:148694400-148741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:148694400-148741200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:148695000-148746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:148709000-148738400	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:148709200-148747600	Weak transcription	Adipose Nuclei	Adipose
10	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:148709600-148741400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:148709800-148747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:148720800-148741400	Weak transcription	Gastric	stomach
14	chr2:148721400-148752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:148721400-148763600	Weak transcription	Spleen	Spleen
16	chr2:148722800-148740400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:148722800-148740600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:148722800-148756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:148725600-148747600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:148726400-148752600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:148726600-148738000	Weak transcription	Dnd41	blood
22	chr2:148726600-148746800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:148726600-148752600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:148727000-148738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:148727200-148740400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:148728200-148773400	Weak transcription	K562	blood
27	chr2:148730800-148740200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:148730800-148740800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:148730800-148742000	Weak transcription	Placenta	Placenta
30	chr2:148730800-148752600	Weak transcription	Primary T cells from cord blood	blood
31	chr2:148731000-148746200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:148731000-148746600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:148731000-148746800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:148731200-148746400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:148731400-148738800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:148731400-148752800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:148733400-148738400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:148735400-148738600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:148735400-148738800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:148735800-148738800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:148735800-148738800	Weak transcription	Right Ventricle	heart
42	chr2:148736000-148738800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:148736000-148741000	Weak transcription	Thymus	Thymus
44	chr2:148736000-148742000	Weak transcription	Psoas Muscle	Psoas
45	chr2:148736000-148776800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:148736200-148738200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:148736200-148740800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:148736200-148741000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:148736200-148741400	Weak transcription	Ovary	ovary
50	chr2:148736200-148743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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