Variant report

Variant	rs12244153
Chromosome Location	chr10:112773661-112773662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112773361..112773861-chr7:2758450..2759306,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11195357	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11195367	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11195378	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11195384	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11195386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11195389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11195392	0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11195393	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11195402	0.81[AFR][1000 genomes]
rs12240492	0.88[AMR][1000 genomes]
rs12245003	1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12248431	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12248632	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12248739	0.84[CHB][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs12249521	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12249906	0.88[YRI][hapmap]
rs12253950	0.84[ASN][1000 genomes]
rs12255335	0.88[AMR][1000 genomes]
rs12256152	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12258923	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12266042	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12267661	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12268160	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12268606	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1327552	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13306146	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1410052	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1538998	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17128099	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes]
rs17128102	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17128270	1.00[CEU][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17128355	0.81[AFR][1000 genomes]
rs1800038	0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3750621	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3750622	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3763691	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4917593	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918610	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4918620	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55879225	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56005122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56302131	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56350255	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72819772	0.94[ASN][1000 genomes]
rs9804245	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1036202	chr10:112726834-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1051595	chr10:112730022-112789048	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1047412	chr10:112747749-112781413	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv948187	chr10:112771501-112773757	Weak transcription Strong transcription	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:112707200-112784200	Weak transcription	Left Ventricle	heart
3	chr10:112723200-112783000	Weak transcription	Small Intestine	intestine
4	chr10:112732600-112789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:112732800-112782800	Weak transcription	Esophagus	oesophagus
6	chr10:112732800-112789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:112738000-112782800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:112738200-112784600	Weak transcription	Ovary	ovary
9	chr10:112738400-112779400	Weak transcription	HepG2	liver
10	chr10:112739200-112774400	Weak transcription	Gastric	stomach
11	chr10:112740400-112791800	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:112744800-112778800	Weak transcription	Hela-S3	cervix
13	chr10:112745600-112777600	Weak transcription	Pancreas	Pancrea
14	chr10:112746000-112783400	Weak transcription	Colonic Mucosa	Colon
15	chr10:112746800-112782800	Weak transcription	Psoas Muscle	Psoas
16	chr10:112747400-112779800	Weak transcription	Fetal Brain Male	brain
17	chr10:112747600-112785200	Weak transcription	Fetal Brain Female	brain
18	chr10:112749200-112789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:112750400-112785000	Weak transcription	A549	lung
20	chr10:112753200-112779200	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:112753200-112779600	Weak transcription	Brain Anterior Caudate	brain
22	chr10:112753200-112782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr10:112753200-112784200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:112753400-112776200	Weak transcription	Lung	lung
25	chr10:112753400-112789600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:112753800-112775000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:112754000-112782000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:112754000-112784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr10:112754400-112782600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr10:112756800-112777800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr10:112757200-112782400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:112757400-112775400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:112758200-112775000	Strong transcription	GM12878-XiMat	blood
34	chr10:112758200-112783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:112760200-112774600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:112761000-112774000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:112761600-112781400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr10:112761600-112782800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr10:112761800-112778200	Weak transcription	Fetal Intestine Small	intestine
40	chr10:112761800-112784200	Weak transcription	Spleen	Spleen
41	chr10:112762400-112780200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr10:112763000-112781600	Weak transcription	Brain Germinal Matrix	brain
43	chr10:112763400-112781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:112763600-112782400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:112764200-112773800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr10:112764400-112783000	Weak transcription	Brain Substantia Nigra	brain
47	chr10:112764800-112778200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:112764800-112782600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:112765000-112776200	Weak transcription	Fetal Stomach	stomach
50	chr10:112765000-112781200	Weak transcription	Thymus	Thymus

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