Variant report

Variant	rs11890605
Chromosome Location	chr2:54415231-54415232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1001296	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1001297	0.96[EUR][1000 genomes]
rs10181309	0.96[EUR][1000 genomes]
rs10195704	0.96[EUR][1000 genomes]
rs10199041	0.81[EUR][1000 genomes]
rs10207892	0.81[EUR][1000 genomes]
rs11884327	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11886475	0.96[EUR][1000 genomes]
rs11889533	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11896279	0.81[EUR][1000 genomes]
rs11897209	0.96[EUR][1000 genomes]
rs11899522	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390377	0.81[EUR][1000 genomes]
rs13395449	0.96[EUR][1000 genomes]
rs13399915	0.96[EUR][1000 genomes]
rs13401548	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13414565	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425337	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17045575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872327	0.96[EUR][1000 genomes]
rs1872328	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2090182	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2357955	0.96[EUR][1000 genomes]
rs4553857	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57045403	0.85[AFR][1000 genomes]
rs57113434	0.90[EUR][1000 genomes]
rs58842028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59531016	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728889	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6742557	0.81[EUR][1000 genomes]
rs6757204	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72908723	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72908725	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72908727	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72908736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935097	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564849	0.93[EUR][1000 genomes]
rs7567556	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567614	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567816	0.96[EUR][1000 genomes]
rs7594400	0.96[EUR][1000 genomes]
rs7604464	0.96[EUR][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	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
12	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
13	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
14	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
15	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
16	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
17	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv961316	chr2:54409849-54427030	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54362000-54416400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:54367400-54416600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:54369600-54416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:54380600-54429200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:54380600-54434400	Weak transcription	Ovary	ovary
6	chr2:54385800-54415800	Weak transcription	Left Ventricle	heart
7	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
8	chr2:54388400-54424600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:54388400-54435000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:54388600-54416600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:54389800-54420000	Weak transcription	Fetal Stomach	stomach
12	chr2:54404200-54433600	Weak transcription	Brain Anterior Caudate	brain
13	chr2:54406400-54419600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:54410000-54420000	Weak transcription	Right Atrium	heart
15	chr2:54411200-54415800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:54411200-54423600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:54411600-54416800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:54411600-54417200	Weak transcription	Right Ventricle	heart
19	chr2:54412200-54422200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:54412600-54422600	Weak transcription	Fetal Lung	lung
21	chr2:54412600-54435000	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:54412800-54417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:54413000-54420000	Weak transcription	Spleen	Spleen
24	chr2:54413200-54415600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:54413400-54415600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:54413600-54416000	Weak transcription	Gastric	stomach
27	chr2:54413800-54417200	Weak transcription	Esophagus	oesophagus
28	chr2:54414200-54416200	Strong transcription	Liver	Liver
29	chr2:54414200-54416200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:54414200-54434600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:54414400-54415400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54414400-54416400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:54414600-54417000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:54414600-54417600	Weak transcription	Lung	lung
35	chr2:54415000-54418200	Weak transcription	Adipose Nuclei	Adipose
36	chr2:54415200-54415600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:54415200-54432400	Weak transcription	Primary B cells from cord blood	blood
38	chr2:54415200-54434200	Weak transcription	Primary T cells from cord blood	blood
39	chr2:54415200-54434400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:54415200-54434600	Weak transcription	HSMMtube	muscle

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