Variant report

Variant	rs11719262
Chromosome Location	chr3:119889300-119889301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119811496..119816423-chr3:119884642..119891818,9	MCF-7	breast:
2	chr3:119888337..119890858-chr3:119891647..119894832,5	MCF-7	breast:
3	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:
4	chr3:119862753..119866394-chr3:119887362..119889316,3	MCF-7	breast:
5	chr3:119811321..119815437-chr3:119887238..119891326,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11709677	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11710115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11926867	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13087908	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs13088757	0.92[CEU][hapmap]
rs13092071	0.92[CEU][hapmap]
rs1488765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830813	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873070	0.84[JPT][hapmap]
rs2014142	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2029609	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs36107695	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732363	0.80[JPT][hapmap]
rs6765483	0.87[ASN][1000 genomes]
rs6783970	0.83[ASN][1000 genomes]
rs7635647	0.85[JPT][hapmap]
rs902793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816153	0.89[CHD][hapmap]
rs9835042	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9844508	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9877813	0.80[CHB][hapmap];0.90[JPT][hapmap]

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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11719262	TMEM39A	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119884200-119890400	Enhancers	Placenta	Placenta
4	chr3:119884600-119890400	Weak transcription	Adipose Nuclei	Adipose
5	chr3:119884800-119895600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
7	chr3:119886200-119892400	Strong transcription	Fetal Brain Female	brain
8	chr3:119886600-119889600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:119887200-119889400	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:119887800-119891400	Enhancers	NHEK	skin
12	chr3:119888000-119889600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:119888000-119891400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:119888000-119891400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:119888200-119890400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr3:119888200-119891200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:119888200-119891200	Enhancers	HMEC	breast
18	chr3:119888400-119889400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:119888400-119890400	Enhancers	Esophagus	oesophagus
20	chr3:119888400-119890600	Enhancers	Hela-S3	cervix
21	chr3:119888400-119892600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
25	chr3:119888600-119890000	Enhancers	A549	lung
26	chr3:119888600-119890200	Weak transcription	Fetal Stomach	stomach
27	chr3:119888600-119891600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:119888600-119892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:119888600-119892600	Enhancers	Osteobl	bone
30	chr3:119888600-119893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:119888800-119889800	Enhancers	NH-A	brain
33	chr3:119888800-119890000	Enhancers	HSMM	muscle
34	chr3:119888800-119891400	Enhancers	NHLF	lung
35	chr3:119889000-119889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:119889200-119890400	Enhancers	Brain Inferior Temporal Lobe	brain

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