Variant report

Variant	rs3897584
Chromosome Location	chr11:113249725-113249726
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:113236279..113238719-chr11:113247616..113250080,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1055075	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1055076	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs1079594	0.82[JPT][hapmap]
rs1079595	0.82[JPT][hapmap]
rs10891541	0.81[ASN][1000 genomes]
rs10891542	0.81[ASN][1000 genomes]
rs10891543	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10891545	0.81[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs10891546	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1124491	0.82[JPT][hapmap]
rs1124492	0.84[CHD][hapmap]
rs17115439	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1800497	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2155464	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2282511	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298489	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298490	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs28712705	0.81[ASN][1000 genomes]
rs4590907	0.81[CHD][hapmap]
rs4601821	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938009	0.84[LWK][hapmap];0.95[YRI][hapmap]
rs4938012	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938013	0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4938014	0.82[CHD][hapmap]
rs4938015	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6278	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs6589375	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7115082	0.81[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7118900	0.87[JPT][hapmap]
rs7123797	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130431	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs719802	0.83[JPT][hapmap]
rs719804	0.95[YRI][hapmap]
rs7945132	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs877138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3897584	TTC12	cis	lung	GTEx
rs3897584	TTC12	cis	Muscle Skeletal	GTEx
rs3897584	TTC12	cis	multi-tissue	Pritchard
rs3897584	TTC12	cis	parietal	SCAN
rs3897584	TTC12	cis	Heart Left Ventricle	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
2	chr11:113239400-113251600	Weak transcription	Aorta	Aorta
3	chr11:113240200-113258400	Weak transcription	Spleen	Spleen
4	chr11:113240800-113255800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr11:113241800-113257800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:113242000-113253000	Weak transcription	Brain Substantia Nigra	brain
7	chr11:113244200-113255800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:113244400-113256400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:113244600-113254600	Weak transcription	HSMM	muscle
10	chr11:113244800-113257400	Weak transcription	Lung	lung
11	chr11:113245600-113254200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:113247400-113250000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:113247600-113250000	Enhancers	HMEC	breast
14	chr11:113247800-113249800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:113247800-113249800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:113247800-113249800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:113247800-113250000	Enhancers	NHEK	skin
18	chr11:113249000-113255200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:113249000-113255400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:113249000-113257400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:113249200-113252800	Weak transcription	HSMMtube	muscle
22	chr11:113249200-113255400	Weak transcription	Placenta	Placenta
23	chr11:113249200-113257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:113249200-113258200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:113249400-113253800	Weak transcription	Fetal Heart	heart
26	chr11:113249400-113255400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:113249600-113252800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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