Variant report

Variant	rs12420528
Chromosome Location	chr11:77672865-77672866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77668893..77671876-chr11:77671949..77673818,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1124590	0.88[CEU][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12419883	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575197	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12575337	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577951	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135969	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1892868	0.90[YRI][hapmap]
rs1968666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186564	0.90[YRI][hapmap]
rs3740681	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3886195	0.91[YRI][hapmap]
rs4245454	0.91[YRI][hapmap]
rs4944176	0.90[YRI][hapmap]
rs4944178	0.90[YRI][hapmap]
rs4944186	0.88[AMR][1000 genomes]
rs4945229	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57491077	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58992562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59363412	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60124679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60143695	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60355295	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60509203	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61201377	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61226220	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61487443	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67194469	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7107903	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72939484	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72941310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941320	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941328	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941334	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941336	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941350	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941354	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7935050	0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7946876	0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12420528	RP11-91P24.6	cis	Artery Tibial	GTEx
rs12420528	RP11-91P24.6	cis	Thyroid	GTEx
rs12420528	AAMDC	cis	Thyroid	GTEx
rs12420528	RP11-91P24.7	cis	Thyroid	GTEx
rs12420528	RSF1	Cis_1M	lymphoblastoid	RTeQTL
rs12420528	AAMDC	cis	Artery Tibial	GTEx
rs12420528	RP11-91P24.7	cis	Artery Tibial	GTEx
rs12420528	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
2	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
3	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
6	chr11:77597800-77690000	Weak transcription	Gastric	stomach
7	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
9	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
14	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:77645000-77680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:77646200-77689600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:77648600-77690000	Weak transcription	Brain Germinal Matrix	brain
19	chr11:77649200-77701200	Weak transcription	NH-A	brain
20	chr11:77655400-77684400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:77656800-77678000	Weak transcription	Right Ventricle	heart
22	chr11:77658600-77689200	Weak transcription	HUVEC	blood vessel
23	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:77663800-77673000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr11:77663800-77673200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr11:77664200-77673400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:77664200-77689400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:77664200-77704000	Weak transcription	NHEK	skin
29	chr11:77665400-77673600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr11:77665600-77673200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:77665800-77689400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:77667600-77684800	Weak transcription	Fetal Kidney	kidney
35	chr11:77667600-77704200	Weak transcription	NHLF	lung
36	chr11:77668400-77675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:77668400-77689600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:77668400-77701200	Weak transcription	Aorta	Aorta
39	chr11:77668600-77680200	Weak transcription	Fetal Stomach	stomach
40	chr11:77668600-77680400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:77668600-77680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:77668600-77690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:77668600-77690000	Weak transcription	Lung	lung
44	chr11:77669000-77680000	Weak transcription	Fetal Intestine Small	intestine
45	chr11:77669400-77673600	Strong transcription	Dnd41	blood
46	chr11:77669600-77673600	Strong transcription	Fetal Thymus	thymus
47	chr11:77670000-77674400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:77670000-77690000	Weak transcription	Spleen	Spleen
49	chr11:77670200-77689800	Weak transcription	HMEC	breast
50	chr11:77670800-77673400	Strong transcription	Primary B cells from cord blood	blood

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