Variant report

Variant	rs12220258
Chromosome Location	chr10:50669820-50669821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50663321..50665073-chr10:50668527..50670258,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1012553	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1012554	0.91[ASN][1000 genomes]
rs10776574	0.80[ASN][1000 genomes]
rs10776576	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857503	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11101137	0.86[CHB][hapmap]
rs11101140	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11101148	0.84[ASN][1000 genomes]
rs11101153	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11101154	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11527799	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11527805	0.81[CHB][hapmap]
rs11594945	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11815415	0.98[ASN][1000 genomes]
rs12217467	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12218455	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12218602	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12220085	0.81[CHB][hapmap]
rs12413113	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs17177717	0.82[CHB][hapmap]
rs1917799	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1924488	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2209281	0.80[ASN][1000 genomes]
rs2222638	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2228524	0.91[ASN][1000 genomes]
rs2228528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281794	0.82[CHB][hapmap]
rs2889771	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3750745	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3750748	0.82[CHB][hapmap]
rs3763728	0.81[ASN][1000 genomes]
rs3793786	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3793788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4012459	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240505	0.80[ASN][1000 genomes]
rs4240507	0.93[ASN][1000 genomes]
rs4240508	0.95[ASN][1000 genomes]
rs4253009	0.85[ASN][1000 genomes]
rs4253013	0.86[CHB][hapmap]
rs4253024	0.91[ASN][1000 genomes]
rs4253043	0.86[CHB][hapmap]
rs4253060	0.86[CHB][hapmap]
rs4253082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4253095	0.83[CHB][hapmap]
rs4253217	0.80[ASN][1000 genomes]
rs4253226	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838518	0.80[ASN][1000 genomes]
rs4838519	0.80[ASN][1000 genomes]
rs56002988	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57761316	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59219652	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61288726	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537537	0.98[ASN][1000 genomes]
rs7080607	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7082895	0.85[ASN][1000 genomes]
rs7087700	0.95[ASN][1000 genomes]
rs7096755	0.81[ASN][1000 genomes]
rs7901433	0.98[ASN][1000 genomes]
rs7907557	0.80[ASN][1000 genomes]
rs932735	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv895377	chr10:50588990-50678212	ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831867	chr10:50607857-50788751	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	17 gene(s)	inside rSNPs	diseases
5	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50656600-50672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:50660400-50672400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:50662200-50677800	Weak transcription	Fetal Heart	heart
4	chr10:50662200-50691600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:50662400-50690000	Weak transcription	Stomach Mucosa	stomach
6	chr10:50662400-50693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:50662600-50670200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:50662600-50670400	Strong transcription	Osteobl	bone
9	chr10:50662600-50674800	Weak transcription	Colonic Mucosa	Colon
10	chr10:50662600-50676600	Weak transcription	Small Intestine	intestine
11	chr10:50662600-50677600	Weak transcription	NHDF-Ad	bronchial
12	chr10:50662600-50691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:50663000-50675800	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:50663200-50672600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:50663200-50693800	Weak transcription	HepG2	liver
16	chr10:50663400-50671200	Strong transcription	HMEC	breast
17	chr10:50663600-50671000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:50663600-50671000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:50663800-50670200	Strong transcription	NHEK	skin
20	chr10:50663800-50671600	Weak transcription	Dnd41	blood
21	chr10:50663800-50672600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:50664000-50677400	Weak transcription	Fetal Kidney	kidney
23	chr10:50664600-50670200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:50664600-50678200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr10:50664800-50670200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr10:50665000-50670000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:50665400-50671000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr10:50665600-50670000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:50665600-50671600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr10:50665800-50672000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:50666200-50672600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:50666200-50674200	Weak transcription	Fetal Brain Male	brain
33	chr10:50666600-50670200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr10:50666600-50670400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr10:50666600-50676400	Weak transcription	K562	blood
36	chr10:50666600-50684400	Weak transcription	NHLF	lung
37	chr10:50666800-50678200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr10:50667200-50672000	Weak transcription	Thymus	Thymus
39	chr10:50667600-50672600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:50667600-50675600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:50667800-50670400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:50667800-50671800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:50667800-50677600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr10:50667800-50707400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:50668000-50713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr10:50668200-50674400	Weak transcription	Fetal Lung	lung
47	chr10:50668200-50675800	Weak transcription	Esophagus	oesophagus
48	chr10:50668200-50680200	Weak transcription	GM12878-XiMat	blood
49	chr10:50668400-50676400	Weak transcription	Hela-S3	cervix
50	chr10:50668400-50677600	Weak transcription	NH-A	brain

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