Variant report

Variant	rs17153622
Chromosome Location	chr10:43890151-43890152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43631919..43634384-chr10:43890115..43892168,2	K562	blood:
2	chr10:43832614..43835578-chr10:43888340..43890232,2	MCF-7	breast:
3	chr10:43845449..43848194-chr10:43889287..43891526,2	K562	blood:
4	chr10:43760797..43762472-chr10:43889762..43891299,2	K562	blood:
5	chr10:43889891..43893674-chr10:43930869..43934431,5	MCF-7	breast:
6	chr10:43887055..43906178-chr10:43946385..43955803,85	K562	blood:
7	chr1:152940729..152943667-chr10:43889848..43892528,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169826	Chromatin interaction
ENSG00000184148	Chromatin interaction
ENSG00000198915	Chromatin interaction
ENSG00000252532	Chromatin interaction
ENSG00000273008	Chromatin interaction
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1112959	0.83[TSI][hapmap]
rs12240317	0.83[TSI][hapmap]
rs12260474	0.83[TSI][hapmap]
rs1338563	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17153606	0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[ASN][1000 genomes]
rs17153617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2248638	1.00[CEU][hapmap]
rs2460559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2493665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2819033	0.83[ASN][1000 genomes]
rs2893915	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322345	0.86[ASN][1000 genomes]
rs4948728	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55693949	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58461087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58723653	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59307177	0.90[ASN][1000 genomes]
rs60241506	0.90[ASN][1000 genomes]
rs61858994	0.95[ASN][1000 genomes]
rs7092125	0.91[ASN][1000 genomes]
rs73253725	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74137742	0.90[ASN][1000 genomes]
rs74137744	0.90[ASN][1000 genomes]
rs74137746	0.90[ASN][1000 genomes]
rs74137748	0.90[ASN][1000 genomes]
rs74137749	0.90[ASN][1000 genomes]
rs74137751	0.90[ASN][1000 genomes]
rs7898074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7900950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7901252	0.90[ASN][1000 genomes]
rs7901608	0.81[ASN][1000 genomes]
rs7907072	0.81[ASN][1000 genomes]
rs7909278	0.90[ASN][1000 genomes]
rs7922334	0.80[EUR][1000 genomes]
rs9919396	0.90[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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
6	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17153622	RP11-517P14.1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43858600-43891000	Weak transcription	Right Atrium	heart
2	chr10:43873200-43890200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:43873400-43891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:43879800-43890600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:43880000-43890200	Strong transcription	Fetal Muscle Leg	muscle
6	chr10:43880000-43890200	Strong transcription	HSMMtube	muscle
7	chr10:43880000-43890400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr10:43880000-43890800	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr10:43880200-43890200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:43880200-43890200	Strong transcription	Osteobl	bone
11	chr10:43880200-43890800	Strong transcription	HSMM	muscle
12	chr10:43880400-43890200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:43880400-43890400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:43880400-43890400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:43880400-43890800	Strong transcription	Hela-S3	cervix
16	chr10:43880600-43890600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:43880600-43890600	Strong transcription	NH-A	brain
18	chr10:43880800-43890200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:43881000-43890400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr10:43881200-43890800	Strong transcription	Lung	lung
21	chr10:43882000-43890200	Strong transcription	Fetal Stomach	stomach
22	chr10:43882000-43890400	Strong transcription	Rectal Smooth Muscle	rectum
23	chr10:43882200-43890400	Strong transcription	NHEK	skin
24	chr10:43882600-43891000	Genic enhancers	Primary T cells fromperipheralblood	blood
25	chr10:43883000-43890400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr10:43883200-43890400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr10:43883200-43890400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr10:43883200-43890600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr10:43883200-43890600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:43883400-43890600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr10:43883600-43890200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr10:43885400-43890400	Strong transcription	Fetal Lung	lung
33	chr10:43885400-43890600	Genic enhancers	Liver	Liver
34	chr10:43885600-43890200	Genic enhancers	Fetal Intestine Large	intestine
35	chr10:43885600-43890200	Genic enhancers	Fetal Intestine Small	intestine
36	chr10:43885600-43890600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:43885800-43890400	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr10:43886200-43890200	Strong transcription	Brain Anterior Caudate	brain
39	chr10:43886400-43890200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:43886400-43890200	Strong transcription	Brain Cingulate Gyrus	brain
41	chr10:43886400-43890400	Strong transcription	Brain Substantia Nigra	brain
42	chr10:43886400-43890400	Strong transcription	Left Ventricle	heart
43	chr10:43887000-43890200	Strong transcription	Placenta	Placenta
44	chr10:43887400-43891200	Genic enhancers	Spleen	Spleen
45	chr10:43888000-43890200	Strong transcription	Brain Angular Gyrus	brain
46	chr10:43888000-43891400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:43888200-43890600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr10:43888400-43890200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:43888400-43890600	Genic enhancers	Primary T cells from cord blood	blood
50	chr10:43888600-43890200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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