Variant report

Variant	rs7925343
Chromosome Location	chr11:77464936-77464937
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	chr11:77458902..77461014-chr11:77463719..77466045,2	MCF-7	breast:
2	chr11:77461975..77464092-chr11:77464635..77466479,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10698394	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10793262	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10793263	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10793264	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899398	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899402	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899403	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899405	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899406	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899407	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899408	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899409	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237289	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237295	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237299	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11237303	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11518811	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12222530	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12364072	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12794428	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1613945	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783546	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1790235	0.90[EUR][1000 genomes]
rs1790240	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790246	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1793334	0.85[EUR][1000 genomes]
rs1793336	0.89[EUR][1000 genomes]
rs1793341	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2212317	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298819	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2510967	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4245453	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4638330	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945198	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945199	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4945201	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4945206	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496786	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574665	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61900164	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7110924	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7128224	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130719	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7358471	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7927913	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7931272	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940734	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9666484	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9988883	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
5	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv976491	chr11:77459085-77487555	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7925343	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77409600-77478200	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77410400-77477600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77431600-77482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:77436200-77473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:77436200-77477000	Weak transcription	Colonic Mucosa	Colon
6	chr11:77436600-77473200	Weak transcription	NHDF-Ad	bronchial
7	chr11:77442400-77472600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:77442800-77474600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:77442800-77500200	Weak transcription	Pancreas	Pancrea
10	chr11:77443000-77465800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:77443200-77473600	Weak transcription	Fetal Brain Female	brain
12	chr11:77443200-77500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:77443800-77465800	Weak transcription	Brain Germinal Matrix	brain
14	chr11:77445800-77476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:77446000-77465800	Weak transcription	Fetal Kidney	kidney
16	chr11:77446200-77465800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:77446200-77467200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:77446200-77482400	Weak transcription	Spleen	Spleen
19	chr11:77446400-77474800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:77447800-77465800	Weak transcription	Adipose Nuclei	Adipose
21	chr11:77448800-77473200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:77449800-77474600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:77450400-77465800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:77450600-77474600	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:77452000-77465000	Weak transcription	Placenta	Placenta
26	chr11:77452000-77465800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:77452000-77465800	Weak transcription	Fetal Brain Male	brain
28	chr11:77452000-77479400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:77452200-77473400	Weak transcription	Hela-S3	cervix
30	chr11:77452200-77481600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:77452600-77474600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:77453200-77473200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:77459000-77474600	Weak transcription	NHLF	lung
34	chr11:77459200-77465800	Weak transcription	HSMMtube	muscle
35	chr11:77459200-77466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:77459200-77472200	Weak transcription	Liver	Liver
37	chr11:77459200-77473200	Weak transcription	HSMM	muscle
38	chr11:77459200-77473400	Weak transcription	HMEC	breast
39	chr11:77459200-77474400	Weak transcription	NH-A	brain
40	chr11:77459400-77498200	Weak transcription	NHEK	skin
41	chr11:77459600-77465600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:77459600-77465600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:77459600-77466000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:77460000-77466000	Weak transcription	Osteobl	bone
45	chr11:77460000-77495800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:77460200-77474600	Weak transcription	HUVEC	blood vessel
47	chr11:77460600-77474600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:77461800-77465400	Enhancers	H9 Cell Line	embryonic stem cell
49	chr11:77462000-77465000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:77462000-77465200	Enhancers	Psoas Muscle	Psoas

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