Variant report

Variant	rs6460795
Chromosome Location	chr7:11277413-11277414
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	chr7:11277040..11279683-chr7:11299557..11301437,2	MCF-7	breast:
2	chr7:11271122..11274578-chr7:11276351..11278199,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10233910	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10242484	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10254173	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258351	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10263230	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10263381	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10263522	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10267548	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950340	0.80[ASN][1000 genomes]
rs11973276	0.80[ASN][1000 genomes]
rs12055949	0.80[ASN][1000 genomes]
rs12534464	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17164105	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58132088	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6460796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069423	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73291706	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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
3	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active 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	30 gene(s)	inside rSNPs	diseases
8	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv1029882	chr7:10872162-11371145	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv428162	chr7:11085784-11359333	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv523279	chr7:11198193-11473561	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv518180	chr7:11198193-11475819	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1015837	chr7:11208733-11475112	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv538732	chr7:11208733-11475112	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv1024940	chr7:11276392-11310923	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6460795	TOB2	trans	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11274800-11283800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:11276200-11278000	Enhancers	Brain Germinal Matrix	brain
3	chr7:11276400-11277800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:11276400-11278000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:11276600-11277800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr7:11276600-11278000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:11276800-11277800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:11277000-11292600	Weak transcription	Stomach Mucosa	stomach
9	chr7:11277200-11277800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:11277200-11277800	Active TSS	Psoas Muscle	Psoas
11	chr7:11277400-11277600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:11277400-11277600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:11277400-11277600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:11277400-11277600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:11277400-11277600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
16	chr7:11277400-11277600	Enhancers	Placenta	Placenta
17	chr7:11277400-11277600	Flanking Active TSS	Gastric	stomach
18	chr7:11277400-11277600	Flanking Active TSS	Left Ventricle	heart
19	chr7:11277400-11277600	Enhancers	Lung	lung
20	chr7:11277400-11277800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr7:11277400-11277800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr7:11277400-11277800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr7:11277400-11277800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:11277400-11277800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:11277400-11277800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:11277400-11277800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr7:11277400-11277800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:11277400-11277800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:11277400-11277800	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr7:11277400-11277800	Flanking Active TSS	Liver	Liver
31	chr7:11277400-11277800	Active TSS	Brain Anterior Caudate	brain
32	chr7:11277400-11277800	Active TSS	Colonic Mucosa	Colon
33	chr7:11277400-11277800	Active TSS	Colon Smooth Muscle	Colon
34	chr7:11277400-11277800	Active TSS	Duodenum Mucosa	Duodenum
35	chr7:11277400-11277800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr7:11277400-11277800	Active TSS	Fetal Intestine Large	intestine
37	chr7:11277400-11277800	Active TSS	Fetal Intestine Small	intestine
38	chr7:11277400-11277800	Enhancers	Ovary	ovary
39	chr7:11277400-11277800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr7:11277400-11277800	Active TSS	Rectal Smooth Muscle	rectum
41	chr7:11277400-11277800	Active TSS	Right Atrium	heart
42	chr7:11277400-11277800	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr7:11277400-11277800	Active TSS	Stomach Smooth Muscle	stomach
44	chr7:11277400-11277800	Active TSS	A549	lung
45	chr7:11277400-11277800	Bivalent/Poised TSS	HepG2	liver
46	chr7:11277400-11277800	Active TSS	NHDF-Ad	bronchial
47	chr7:11277400-11277800	Active TSS	Osteobl	bone
48	chr7:11277400-11278000	Active TSS	HUVEC	blood vessel

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