Variant report

Variant	rs60509203
Chromosome Location	chr11:77641359-77641360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1124590	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12417760	0.80[EUR][1000 genomes]
rs12418551	0.80[EUR][1000 genomes]
rs12419883	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12420290	0.80[EUR][1000 genomes]
rs12420528	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12574507	0.80[EUR][1000 genomes]
rs12575197	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12575337	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12577951	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17135905	0.80[EUR][1000 genomes]
rs17135969	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1968666	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2032415	0.80[EUR][1000 genomes]
rs2051484	0.80[EUR][1000 genomes]
rs3740681	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758664	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886195	0.80[EUR][1000 genomes]
rs4245454	0.83[EUR][1000 genomes]
rs4245455	0.84[EUR][1000 genomes]
rs4448713	0.80[EUR][1000 genomes]
rs4491258	0.80[EUR][1000 genomes]
rs4944176	0.80[EUR][1000 genomes]
rs4944178	0.80[EUR][1000 genomes]
rs4944186	0.87[AMR][1000 genomes]
rs4945223	0.80[EUR][1000 genomes]
rs4945229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4945230	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57491077	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58020660	0.81[EUR][1000 genomes]
rs58992562	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59239088	0.83[EUR][1000 genomes]
rs59363412	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60124679	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60143695	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60208812	0.80[EUR][1000 genomes]
rs60355295	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61201377	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61226220	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61487443	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61605540	0.83[EUR][1000 genomes]
rs67194469	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7107903	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110322	0.80[EUR][1000 genomes]
rs72939448	0.80[EUR][1000 genomes]
rs72939452	0.84[EUR][1000 genomes]
rs72939456	0.83[EUR][1000 genomes]
rs72939484	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72941310	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72941320	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72941328	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72941334	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72941336	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72941350	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72941354	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7935050	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7946876	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs60509203	RP11-91P24.6	cis	Thyroid	GTEx
rs60509203	AAMDC	cis	Thyroid	GTEx
rs60509203	AAMDC	cis	Artery Tibial	GTEx
rs60509203	RP11-91P24.7	cis	Artery Tibial	GTEx
rs60509203	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs60509203	RP11-91P24.6	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 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	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
5	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
10	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
13	chr11:77597800-77690000	Weak transcription	Gastric	stomach
14	chr11:77602600-77644200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:77603200-77650200	Weak transcription	Fetal Brain Female	brain
17	chr11:77604800-77644200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
19	chr11:77615000-77644200	Weak transcription	Spleen	Spleen
20	chr11:77615000-77656400	Weak transcription	Right Ventricle	heart
21	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:77618800-77644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
24	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:77620800-77642000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:77625800-77665600	Weak transcription	HSMMtube	muscle
27	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:77626000-77666200	Weak transcription	Brain Substantia Nigra	brain
29	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:77626200-77641600	Weak transcription	Osteobl	bone
31	chr11:77626200-77665400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:77626600-77644800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:77626600-77665600	Weak transcription	Ovary	ovary
35	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
37	chr11:77627000-77642000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:77627000-77645200	Weak transcription	HepG2	liver
39	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:77628000-77646000	Weak transcription	Primary T cells from cord blood	blood
41	chr11:77628000-77671000	Weak transcription	HSMM	muscle
42	chr11:77628400-77668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:77629400-77653400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr11:77629400-77668000	Weak transcription	Aorta	Aorta
45	chr11:77630000-77648000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:77630000-77665400	Weak transcription	Lung	lung
47	chr11:77630200-77669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr11:77630400-77641600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:77630400-77642600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:77630600-77665400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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