Variant report

Variant	rs12575197
Chromosome Location	chr11:77665728-77665729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1124590	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11825573	0.81[CEU][hapmap]
rs12417488	0.81[CEU][hapmap]
rs12419883	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12420401	0.81[CEU][hapmap]
rs12420528	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12575337	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12577951	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135969	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1892869	0.81[CEU][hapmap]
rs1893901	0.81[CEU][hapmap]
rs1968666	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740681	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3758664	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886195	0.81[CEU][hapmap]
rs4245454	0.81[CEU][hapmap]
rs4944186	0.84[AMR][1000 genomes]
rs4945211	0.81[CEU][hapmap]
rs4945219	0.81[CEU][hapmap]
rs4945223	0.81[CEU][hapmap]
rs4945229	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4945230	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57491077	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58992562	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59363412	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60124679	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60143695	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60355295	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60509203	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61201377	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61226220	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61487443	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67194469	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7104540	0.90[CEU][hapmap]
rs7106113	0.81[CEU][hapmap]
rs7107903	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7124116	0.83[CEU][hapmap]
rs7127803	0.81[CEU][hapmap]
rs72939484	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72941310	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941320	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941328	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941336	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941350	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941354	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7930066	0.81[CEU][hapmap]
rs7931215	0.81[CEU][hapmap]
rs7935050	0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7936904	0.83[CEU][hapmap]
rs7937983	0.83[CEU][hapmap]
rs7946876	0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7951172	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv975205	chr11:77628075-77671380	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv8841	chr11:77641044-77692578	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12575197	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs12575197	RSF1	Cis_1M	lymphoblastoid	RTeQTL
rs12575197	RP11-91P24.6	cis	Thyroid	GTEx
rs12575197	AAMDC	cis	Thyroid	GTEx
rs12575197	RP11-91P24.6	cis	Artery Tibial	GTEx
rs12575197	RP11-91P24.7	cis	Artery Tibial	GTEx
rs12575197	AAMDC	cis	Artery Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
3	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
4	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
7	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
10	chr11:77597800-77690000	Weak transcription	Gastric	stomach
11	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
13	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
15	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:77626000-77666200	Weak transcription	Brain Substantia Nigra	brain
18	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
22	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr11:77628000-77671000	Weak transcription	HSMM	muscle
24	chr11:77628400-77668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:77629400-77668000	Weak transcription	Aorta	Aorta
26	chr11:77630200-77669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:77639400-77667000	Weak transcription	Fetal Lung	lung
28	chr11:77639400-77670200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:77639800-77668000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:77640000-77667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:77641200-77669600	Weak transcription	K562	blood
32	chr11:77641600-77671000	Weak transcription	Hela-S3	cervix
33	chr11:77642200-77668000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:77644600-77667200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:77644800-77667400	Weak transcription	Spleen	Spleen
36	chr11:77645000-77666200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:77645000-77667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:77645000-77680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:77646200-77689600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:77646400-77667000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:77648000-77670600	Weak transcription	GM12878-XiMat	blood
43	chr11:77648600-77690000	Weak transcription	Brain Germinal Matrix	brain
44	chr11:77648800-77666200	Weak transcription	Fetal Thymus	thymus
45	chr11:77648800-77667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:77649000-77668000	Weak transcription	Primary T cells from cord blood	blood
47	chr11:77649200-77701200	Weak transcription	NH-A	brain
48	chr11:77651600-77666400	Weak transcription	Liver	Liver
49	chr11:77654400-77670600	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:77655000-77670600	Weak transcription	NHDF-Ad	bronchial

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