Variant report

Variant	rs2154972
Chromosome Location	chr11:77488825-77488826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77488267..77490535-chr11:77493652..77495345,2	K562	blood:
2	chr11:77487445..77490849-chr11:77530264..77533102,3	MCF-7	breast:
3	chr11:77488328..77491203-chr11:77709162..77710811,2	K562	blood:

Variant related genes	Relation type
ENSG00000087884	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10899399	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899404	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237263	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237280	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237318	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11600140	0.81[EUR][1000 genomes]
rs11603438	0.84[EUR][1000 genomes]
rs11606549	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12285765	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12286317	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17752006	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1783544	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs24356	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2508189	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34130561	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4322421	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344516	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484363	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4945220	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs537811	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56218634	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588217	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs598071	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614495	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs621456	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs623173	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs623907	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635195	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636971	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643388	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs648601	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs648896	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs650171	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663674	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667225	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs668701	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs670090	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684813	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs687037	0.90[EUR][1000 genomes]
rs694845	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs695046	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7122968	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72945592	0.92[ASN][1000 genomes]
rs72945598	0.82[EUR][1000 genomes]
rs72947625	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72947668	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72949616	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72949618	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7950873	0.84[EUR][1000 genomes]
rs7951033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947841	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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	esv3427950	chr11:77488129-77490677	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2154972	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77442800-77500200	Weak transcription	Pancreas	Pancrea
2	chr11:77443200-77500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:77459400-77498200	Weak transcription	NHEK	skin
4	chr11:77460000-77495800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:77462200-77500200	Weak transcription	Gastric	stomach
6	chr11:77463800-77527000	Weak transcription	Aorta	Aorta
7	chr11:77465200-77500200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:77467000-77500200	Weak transcription	Esophagus	oesophagus
9	chr11:77475200-77495600	Weak transcription	Fetal Intestine Large	intestine
10	chr11:77475200-77498000	Weak transcription	HMEC	breast
11	chr11:77475200-77501600	Weak transcription	Brain Germinal Matrix	brain
12	chr11:77475200-77502600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:77475200-77527800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:77475400-77489000	Weak transcription	HSMM	muscle
15	chr11:77475400-77489600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:77475400-77490800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:77475400-77495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:77475400-77500400	Weak transcription	Lung	lung
19	chr11:77475400-77500600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:77475400-77501800	Weak transcription	Thymus	Thymus
21	chr11:77475400-77502400	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:77475400-77504200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:77475400-77522000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:77475400-77529000	Weak transcription	NHLF	lung
25	chr11:77475400-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:77475600-77491000	Weak transcription	NH-A	brain
27	chr11:77475600-77495200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr11:77475600-77498000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:77475600-77498200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:77475600-77500200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:77475600-77511600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:77475600-77511600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:77475800-77491000	Weak transcription	Fetal Brain Female	brain
34	chr11:77475800-77494400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:77475800-77510400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:77475800-77522000	Weak transcription	Hela-S3	cervix
37	chr11:77476800-77495800	Weak transcription	Small Intestine	intestine
38	chr11:77478400-77489600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:77478600-77498600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:77478800-77491200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:77478800-77495600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:77482400-77489000	Weak transcription	Stomach Mucosa	stomach
43	chr11:77482400-77490000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:77482600-77489400	Weak transcription	Brain Substantia Nigra	brain
45	chr11:77482600-77489600	Weak transcription	K562	blood
46	chr11:77482600-77495200	Weak transcription	Fetal Thymus	thymus
47	chr11:77482600-77495600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:77482600-77500200	Weak transcription	Right Ventricle	heart
49	chr11:77482600-77509800	Weak transcription	Adipose Nuclei	Adipose
50	chr11:77482800-77495800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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