Variant report

Variant	rs623907
Chromosome Location	chr11:77501448-77501449
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77492334..77494462-chr11:77499112..77501591,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10899399	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899404	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237263	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237280	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237318	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11600140	0.82[EUR][1000 genomes]
rs11603438	0.82[EUR][1000 genomes]
rs11606549	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12285765	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12286317	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17752006	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783544	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2154972	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs24356	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508189	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34130561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4322421	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344516	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484363	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4945220	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs537811	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56218634	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588217	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs598071	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614495	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs621456	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs623173	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs635195	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636971	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643388	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648601	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs648896	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs650171	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663674	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667225	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs668701	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs670090	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684813	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs687037	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs694845	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695046	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7122968	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123080	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945592	0.92[ASN][1000 genomes]
rs72945598	0.80[EUR][1000 genomes]
rs72947625	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72947668	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72949616	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72949618	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7950873	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7951033	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947841	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs623907	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77463800-77527000	Weak transcription	Aorta	Aorta
2	chr11:77475200-77501600	Weak transcription	Brain Germinal Matrix	brain
3	chr11:77475200-77502600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:77475200-77527800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:77475400-77501800	Weak transcription	Thymus	Thymus
6	chr11:77475400-77502400	Weak transcription	Fetal Muscle Leg	muscle
7	chr11:77475400-77504200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:77475400-77522000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:77475400-77529000	Weak transcription	NHLF	lung
10	chr11:77475400-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:77475600-77511600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:77475600-77511600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:77475800-77510400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:77475800-77522000	Weak transcription	Hela-S3	cervix
15	chr11:77482600-77509800	Weak transcription	Adipose Nuclei	Adipose
16	chr11:77482800-77501800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:77482800-77525800	Weak transcription	Fetal Lung	lung
18	chr11:77487200-77501600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:77487200-77503200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:77487400-77503000	Weak transcription	Dnd41	blood
21	chr11:77487400-77522000	Weak transcription	Placenta	Placenta
22	chr11:77489800-77503400	Weak transcription	A549	lung
23	chr11:77489800-77511600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:77491400-77517600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:77493600-77501800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:77494600-77503000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr11:77495800-77528200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:77496000-77530200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:77496200-77502200	Weak transcription	Fetal Intestine Large	intestine
30	chr11:77496200-77503400	Weak transcription	Primary B cells from cord blood	blood
31	chr11:77496400-77503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:77497200-77506200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:77498000-77504600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:77498200-77502000	Weak transcription	HepG2	liver
35	chr11:77498800-77504000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:77498800-77504000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:77498800-77510200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:77499000-77525600	Weak transcription	HMEC	breast
39	chr11:77499200-77506000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:77499200-77511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:77499200-77513800	Weak transcription	NHEK	skin
42	chr11:77500000-77511400	Weak transcription	Fetal Heart	heart
43	chr11:77500200-77502600	Weak transcription	Primary T cells from cord blood	blood
44	chr11:77500200-77505800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:77500400-77501800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:77500400-77502400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:77500400-77505400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:77500400-77512200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:77500600-77501800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:77500600-77501800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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