Variant report

Variant	rs7909072
Chromosome Location	chr10:96995971-96995972
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	chr10:96989917..96992480-chr10:96995874..96997561,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234026	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10128123	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10218877	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs10509683	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10882566	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs10882568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10882569	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882570	0.95[ASN][1000 genomes]
rs10882571	0.95[ASN][1000 genomes]
rs11188223	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs11188225	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs11188227	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11188228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11188229	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11188230	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11188236	0.92[ASN][1000 genomes]
rs11188238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11188239	0.95[ASN][1000 genomes]
rs11188240	0.95[ASN][1000 genomes]
rs11596737	0.81[CEU][hapmap];0.93[CHD][hapmap]
rs11596853	0.81[CEU][hapmap]
rs11598953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs11598991	0.87[ASN][1000 genomes]
rs11599546	0.95[ASN][1000 genomes]
rs11599884	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11872	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12245722	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12262534	0.92[ASN][1000 genomes]
rs12262878	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12413028	0.92[CEU][hapmap];0.93[CHD][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs12415795	0.92[CEU][hapmap];0.93[CHD][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs12764831	1.00[JPT][hapmap]
rs12769820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12783947	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12784385	0.92[ASN][1000 genomes]
rs16872	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs17524438	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2449809	1.00[JPT][hapmap]
rs2478477	1.00[JPT][hapmap]
rs2478478	1.00[JPT][hapmap]
rs2478479	1.00[JPT][hapmap]
rs3210020	0.86[ASN][1000 genomes]
rs35999600	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45510800	0.86[ASN][1000 genomes]
rs45605435	0.86[ASN][1000 genomes]
rs489807	1.00[JPT][hapmap]
rs509736	1.00[JPT][hapmap]
rs513661	1.00[JPT][hapmap]
rs589801	1.00[JPT][hapmap]
rs591157	1.00[JPT][hapmap]
rs591171	1.00[JPT][hapmap]
rs592055	1.00[JPT][hapmap]
rs594448	1.00[JPT][hapmap]
rs610046	1.00[JPT][hapmap]
rs611343	1.00[JPT][hapmap]
rs612490	1.00[JPT][hapmap]
rs613340	1.00[JPT][hapmap]
rs614682	1.00[JPT][hapmap]
rs61871367	0.91[EUR][1000 genomes]
rs626415	1.00[JPT][hapmap]
rs627173	1.00[JPT][hapmap]
rs628102	1.00[JPT][hapmap]
rs633345	1.00[JPT][hapmap]
rs637465	1.00[JPT][hapmap]
rs648695	1.00[JPT][hapmap]
rs659949	1.00[JPT][hapmap]
rs664093	1.00[JPT][hapmap]
rs672860	1.00[JPT][hapmap]
rs685607	1.00[JPT][hapmap]
rs688706	1.00[JPT][hapmap]
rs689207	1.00[JPT][hapmap]
rs695217	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7089303	1.00[JPT][hapmap]
rs7924214	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv21432	chr10:96856006-96996043	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7909072	PIPSL	cis	cerebellum	SCAN
rs7909072	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96990800-96997400	Weak transcription	Stomach Mucosa	stomach
2	chr10:96990800-97005200	Weak transcription	Psoas Muscle	Psoas
3	chr10:96991000-96996000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:96991000-96996200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr10:96991000-96996400	Weak transcription	Right Ventricle	heart
6	chr10:96991000-96997200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:96991000-96997400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr10:96991000-96997600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:96991000-96999800	Weak transcription	Fetal Lung	lung
10	chr10:96991000-97001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:96991000-97001600	Weak transcription	Thymus	Thymus
12	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:96991000-97006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:96991000-97006600	Weak transcription	Colon Smooth Muscle	Colon
16	chr10:96991000-97006600	Weak transcription	Right Atrium	heart
17	chr10:96991000-97007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr10:96991000-97020400	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:96991200-96996400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:96991200-97000000	Weak transcription	Fetal Kidney	kidney
22	chr10:96991200-97000200	Weak transcription	Fetal Thymus	thymus
23	chr10:96991400-97019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:96991600-96996200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr10:96991600-96997400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:96991600-97001000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr10:96992000-97005000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr10:96992000-97005800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:96992200-96997400	Weak transcription	Small Intestine	intestine
30	chr10:96992200-97009000	Strong transcription	Liver	Liver
31	chr10:96992400-96996000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr10:96992400-96996200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:96992400-96996200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr10:96992400-96998600	Strong transcription	Fetal Stomach	stomach
35	chr10:96992400-96998800	Strong transcription	Left Ventricle	heart
36	chr10:96992400-96999000	Strong transcription	Adipose Nuclei	Adipose
37	chr10:96992400-97000000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:96992400-97006200	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr10:96992600-96998600	Strong transcription	Lung	lung
40	chr10:96992600-97004000	Strong transcription	Fetal Intestine Large	intestine
41	chr10:96993000-96996600	Enhancers	NHDF-Ad	bronchial
42	chr10:96993000-96996800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:96993200-96998800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:96993800-96996200	Weak transcription	Esophagus	oesophagus
45	chr10:96994000-96996200	Weak transcription	Aorta	Aorta
46	chr10:96994200-96996200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr10:96994200-96997400	Weak transcription	Pancreas	Pancrea
48	chr10:96994600-96996000	Enhancers	Osteobl	bone
49	chr10:96994600-96996600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr10:96994600-96996600	Genic enhancers	HUES64 Cell Line	embryonic stem cell

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