Variant report

Variant	rs12219692
Chromosome Location	chr10:52323909-52323910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52321910..52324715-chr10:52371827..52374232,3	K562	blood:
2	chr10:52322894..52324648-chr10:52337430..52339164,2	K562	blood:
3	chr10:52318973..52324648-chr10:52334040..52339164,5	K562	blood:
4	chr10:52319893..52329540-chr10:52377624..52388129,20	MCF-7	breast:
5	chr10:52323633..52328946-chr10:52382781..52388541,7	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10508927	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10763382	1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10763535	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs10763550	0.83[CEU][hapmap];0.85[MEX][hapmap]
rs10763566	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs10825882	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10825904	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10825934	0.90[AFR][1000 genomes]
rs10825978	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10826033	0.81[AFR][1000 genomes]
rs10826036	0.81[AFR][1000 genomes]
rs10826161	0.94[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10826166	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs10826169	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10826170	0.89[EUR][1000 genomes]
rs11005356	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11005418	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11005579	0.92[CEU][hapmap];0.90[AFR][1000 genomes]
rs11005614	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11005621	0.90[AFR][1000 genomes]
rs11006054	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11006075	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006084	0.94[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs11006114	0.94[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs11006118	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs11006217	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs12217648	0.90[AFR][1000 genomes]
rs12415817	0.94[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12415836	0.89[EUR][1000 genomes]
rs12572387	0.83[CEU][hapmap]
rs1916572	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2024872	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144861	0.94[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs3001883	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs34122137	0.90[AFR][1000 genomes]
rs34659292	0.90[EUR][1000 genomes]
rs36122110	0.90[EUR][1000 genomes]
rs3739989	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4519042	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4519043	0.81[ASN][1000 genomes]
rs4935173	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs4935174	0.94[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs4935728	0.82[AMR][1000 genomes]
rs6481461	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7067552	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7074764	0.83[CEU][hapmap]
rs7086029	1.00[ASW][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7088141	0.83[CEU][hapmap]
rs7089882	1.00[YRI][hapmap]
rs7094143	0.90[EUR][1000 genomes]
rs7907260	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7920818	0.95[MEX][hapmap]
rs7922802	0.80[MEX][hapmap]
rs927048	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9919413	0.94[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
6	chr10:52310600-52327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
8	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr10:52315000-52329600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:52315200-52337400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr10:52315600-52336000	Weak transcription	GM12878-XiMat	blood
15	chr10:52316400-52325200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr10:52316400-52327200	Weak transcription	Fetal Muscle Leg	muscle
17	chr10:52316400-52331800	Weak transcription	Lung	lung
18	chr10:52316800-52332000	Weak transcription	Aorta	Aorta
19	chr10:52316800-52332600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr10:52318200-52331800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:52318400-52329600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:52319200-52335800	Weak transcription	Spleen	Spleen
23	chr10:52319600-52335600	Weak transcription	NHEK	skin
24	chr10:52320400-52325400	Enhancers	Liver	Liver
25	chr10:52321200-52325200	Weak transcription	Right Ventricle	heart
26	chr10:52321400-52324600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr10:52321400-52326000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr10:52321600-52325200	Weak transcription	Brain Substantia Nigra	brain
29	chr10:52321600-52325800	Weak transcription	HMEC	breast
30	chr10:52321600-52327200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:52321600-52335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:52321800-52325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:52321800-52325400	Weak transcription	Ovary	ovary
34	chr10:52321800-52325400	Weak transcription	Right Atrium	heart
35	chr10:52321800-52325600	Weak transcription	Brain Anterior Caudate	brain
36	chr10:52321800-52326600	Weak transcription	Fetal Brain Female	brain
37	chr10:52321800-52327200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:52321800-52327200	Weak transcription	Brain Germinal Matrix	brain
39	chr10:52321800-52327200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr10:52321800-52331600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:52321800-52331600	Weak transcription	Psoas Muscle	Psoas
42	chr10:52321800-52335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:52321800-52335600	Weak transcription	Adipose Nuclei	Adipose
44	chr10:52322000-52325400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr10:52322000-52327200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:52322000-52330200	Weak transcription	Hela-S3	cervix
47	chr10:52322000-52331000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr10:52322000-52335800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr10:52322000-52337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:52322000-52348600	Weak transcription	Fetal Stomach	stomach

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