Variant report

Variant	rs12613807
Chromosome Location	chr2:191343763-191343764
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10182754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10193212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10931452	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473460	0.83[YRI][hapmap]
rs12475614	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613365	0.83[YRI][hapmap]
rs12622496	0.87[YRI][hapmap]
rs12693574	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693575	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693576	0.83[YRI][hapmap]
rs12998288	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13019278	0.83[YRI][hapmap]
rs13020324	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13409841	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354878	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35095338	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811607	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3811609	0.83[YRI][hapmap]
rs4264585	0.83[YRI][hapmap]
rs4324342	0.83[YRI][hapmap]
rs4340549	0.85[LWK][hapmap]
rs4853507	0.87[ASN][1000 genomes]
rs4853702	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4853705	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4853713	0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434391	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707691	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707773	0.83[YRI][hapmap]
rs6711006	0.83[YRI][hapmap]
rs7557681	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7564829	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7596573	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7603607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646748	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9646815	0.85[EUR][1000 genomes];0.92[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	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12613807	TMEM194B	cis	Adipose Subcutaneous	GTEx
rs12613807	FLJ20160	cis	multi-tissue	Pritchard
rs12613807	HIBCH	cis	cerebellum	SCAN
rs12613807	MFSD6	cis	lymphoblastoid	seeQTL
rs12613807	ZC3H15	cis	cerebellum	SCAN
rs12613807	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs12613807	MFSD6	cis	parietal	SCAN
rs12613807	MFSD6	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
3	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
4	chr2:191332800-191356200	Weak transcription	Aorta	Aorta
5	chr2:191332800-191364200	Weak transcription	Spleen	Spleen
6	chr2:191333400-191355400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:191334200-191370200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:191334400-191351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:191334400-191352800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:191334400-191353400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:191334400-191355400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:191334600-191348800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:191334800-191353200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:191334800-191394800	Weak transcription	HSMMtube	muscle
15	chr2:191335200-191353000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:191335200-191353600	Weak transcription	GM12878-XiMat	blood
17	chr2:191335400-191346000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:191335400-191353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:191335400-191366200	Weak transcription	Hela-S3	cervix
20	chr2:191335600-191353000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:191336000-191354200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:191336200-191346200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:191336200-191346600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:191336600-191346200	Weak transcription	Fetal Thymus	thymus
25	chr2:191336600-191346400	Weak transcription	Thymus	Thymus
26	chr2:191336600-191348600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:191336600-191348800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:191336600-191353000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:191336600-191353000	Weak transcription	Dnd41	blood
30	chr2:191336600-191353200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:191336600-191353600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:191336800-191353000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:191342400-191343800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:191342400-191343800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:191342400-191344000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:191342400-191344000	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr2:191342600-191343800	Strong transcription	Primary T cells from cord blood	blood
38	chr2:191342600-191344000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:191342800-191344000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:191342800-191346600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:191342800-191356000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:191343000-191343800	Enhancers	Fetal Intestine Large	intestine
43	chr2:191343000-191346600	Weak transcription	Right Atrium	heart
44	chr2:191343000-191348800	Weak transcription	A549	lung
45	chr2:191343000-191350800	Weak transcription	Psoas Muscle	Psoas
46	chr2:191343000-191353200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:191343000-191372000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:191343200-191343800	Enhancers	Ovary	ovary
49	chr2:191343200-191345200	Weak transcription	Stomach Mucosa	stomach
50	chr2:191343200-191346200	Weak transcription	Gastric	stomach

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