Variant report

Variant	rs12262249
Chromosome Location	chr10:90644571-90644572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11202877	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202878	0.83[AFR][1000 genomes]
rs11202880	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202881	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12245525	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12245668	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12248501	0.84[AFR][1000 genomes]
rs12254451	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12263461	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12264141	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269097	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113606	0.93[EUR][1000 genomes]
rs1887025	0.93[EUR][1000 genomes]
rs1926184	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926185	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1926186	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55885377	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57063754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57261011	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7076879	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7077019	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7090604	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs74147302	0.89[ASN][1000 genomes]
rs74150105	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7910708	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7913997	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs952323	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641000-90645400	Enhancers	Small Intestine	intestine
2	chr10:90641000-90646400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:90641000-90647200	Weak transcription	Spleen	Spleen
4	chr10:90641000-90653600	Weak transcription	Gastric	stomach
5	chr10:90641400-90644800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:90641400-90645200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr10:90641400-90646400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
9	chr10:90641600-90645800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr10:90641600-90646600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:90641600-90653200	Weak transcription	Colonic Mucosa	Colon
12	chr10:90641800-90646400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:90641800-90647400	Weak transcription	Ovary	ovary
14	chr10:90641800-90653800	Weak transcription	Stomach Mucosa	stomach
15	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
17	chr10:90642000-90646600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:90642000-90648800	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:90642000-90650400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr10:90642000-90651000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:90642200-90648000	Weak transcription	Fetal Muscle Leg	muscle
24	chr10:90642200-90648400	Enhancers	Primary T cells from cord blood	blood
25	chr10:90642200-90648800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr10:90642200-90649800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:90642400-90646400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:90642400-90647400	Weak transcription	Fetal Thymus	thymus
30	chr10:90642400-90648200	Weak transcription	Adipose Nuclei	Adipose
31	chr10:90642400-90651200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:90642400-90652000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:90642600-90645200	Genic enhancers	Dnd41	blood
34	chr10:90642600-90646200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:90642600-90646400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:90642600-90648000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:90642600-90649200	Weak transcription	Primary B cells from cord blood	blood
38	chr10:90642600-90653800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:90643000-90644600	Genic enhancers	Hela-S3	cervix
41	chr10:90643000-90644800	Flanking Active TSS	NHLF	lung
42	chr10:90643000-90645400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:90643200-90645600	Flanking Active TSS	GM12878-XiMat	blood
44	chr10:90643200-90651800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:90643400-90645000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:90643400-90645200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr10:90643400-90645600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr10:90643400-90646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:90643400-90647000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:90643400-90647600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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