Variant report

Variant	rs12613209
Chromosome Location	chr2:20162971-20162972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10169398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208878	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888045	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11889206	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052274	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415707	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421472	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs1381817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16987265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28477921	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502265	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35957485	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109404	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109406	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109413	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109415	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109418	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109419	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109420	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109421	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755153	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7589478	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12613209	TTC32	cis	Stomach	GTEx
rs12613209	LOC130502	cis	multi-tissue	Pritchard
rs12613209	TTC32	cis	multi-tissue	Pritchard
rs12613209	TTC32	cis	Esophagus Muscularis	GTEx
rs12613209	TTC32	cis	lung	GTEx
rs12613209	TTC32	cis	Heart Left Ventricle	GTEx
rs12613209	TTC32	cis	Esophagus Mucosa	GTEx
rs12613209	TTC32	cis	Adipose Subcutaneous	GTEx
rs12613209	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs12613209	TTC32	cis	Thyroid	GTEx
rs12613209	TTC32	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
6	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
7	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:20130400-20164600	Weak transcription	Lung	lung
10	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:20133600-20164800	Weak transcription	Gastric	stomach
14	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
15	chr2:20133800-20173200	Weak transcription	NHEK	skin
16	chr2:20133800-20176800	Weak transcription	HMEC	breast
17	chr2:20134200-20168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
19	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:20136600-20171200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:20136800-20171400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:20137600-20165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:20137800-20165000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:20138000-20165000	Weak transcription	Fetal Brain Female	brain
28	chr2:20138000-20177000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:20138200-20164200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:20138200-20165000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:20138200-20165000	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:20138200-20171400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:20138400-20164400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:20138400-20167800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:20138600-20165000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:20138600-20165000	Weak transcription	Left Ventricle	heart
38	chr2:20138600-20165400	Weak transcription	Osteobl	bone
39	chr2:20138600-20184800	Weak transcription	Aorta	Aorta
40	chr2:20138800-20164800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:20138800-20165000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:20138800-20165000	Weak transcription	Fetal Thymus	thymus
43	chr2:20141600-20163800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:20144600-20173200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:20144600-20173400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:20144600-20173600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:20144800-20168600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:20145000-20168600	Weak transcription	Primary B cells from cord blood	blood
49	chr2:20145000-20176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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