Variant report

Variant	rs11006222
Chromosome Location	chr10:52349283-52349284
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	chr10:52345136..52347979-chr10:52349121..52350897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251950	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10508931	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006166	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006179	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006183	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006185	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11006190	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006191	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006193	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006194	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11006197	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006200	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006213	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11006219	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006229	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006233	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006237	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006238	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496403	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496500	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011801	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55841709	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7072826	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7099133	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921226	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52336800-52363000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:52337800-52352800	Weak transcription	Fetal Brain Male	brain
3	chr10:52338000-52356400	Weak transcription	Fetal Brain Female	brain
4	chr10:52338000-52363800	Weak transcription	Fetal Kidney	kidney
5	chr10:52338000-52367000	Weak transcription	Aorta	Aorta
6	chr10:52338200-52353600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:52338200-52353800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr10:52338600-52353400	Weak transcription	Brain Germinal Matrix	brain
9	chr10:52338600-52353600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:52340400-52360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr10:52341200-52373000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr10:52341400-52355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:52341400-52360200	Weak transcription	GM12878-XiMat	blood
14	chr10:52341800-52350600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:52341800-52351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:52341800-52352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:52341800-52355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:52341800-52362000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:52342000-52352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:52342200-52351800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:52342400-52351600	Weak transcription	Brain Angular Gyrus	brain
22	chr10:52342400-52353000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:52342600-52356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:52342800-52360200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:52343000-52353000	Weak transcription	Fetal Heart	heart
26	chr10:52343400-52360600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr10:52343600-52356200	Weak transcription	Stomach Mucosa	stomach
28	chr10:52343600-52362200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:52343800-52360000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:52344400-52349800	Strong transcription	Primary B cells from cord blood	blood
31	chr10:52345000-52350000	Strong transcription	Primary T cells from cord blood	blood
32	chr10:52345000-52353000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr10:52346000-52349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52346000-52349600	Strong transcription	Ovary	ovary
35	chr10:52346000-52355400	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:52346200-52349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:52346200-52349600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:52346200-52350000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr10:52346400-52349600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr10:52346400-52358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr10:52346600-52350600	Weak transcription	Pancreas	Pancrea
42	chr10:52346600-52351000	Weak transcription	Right Ventricle	heart
43	chr10:52346600-52351800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:52346600-52351800	Weak transcription	Right Atrium	heart
45	chr10:52346600-52352600	Weak transcription	HSMMtube	muscle
46	chr10:52346600-52352600	Weak transcription	NHDF-Ad	bronchial
47	chr10:52346600-52352800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:52346600-52355400	Weak transcription	Psoas Muscle	Psoas
49	chr10:52346600-52363400	Weak transcription	Adipose Nuclei	Adipose
50	chr10:52346600-52363800	Weak transcription	Spleen	Spleen

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