Variant report

Variant	rs16987297
Chromosome Location	chr2:20219369-20219370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20214554..20219540-chr2:20268505..20271599,4	MCF-7	breast:
2	chr2:20206907..20208967-chr2:20217297..20219673,2	MCF-7	breast:
3	chr2:20212605..20214922-chr2:20216980..20220655,3	MCF-7	breast:
4	chr2:20218756..20221372-chr2:20222050..20225276,4	MCF-7	breast:
5	chr2:20218001..20219719-chr2:20249053..20251936,2	MCF-7	breast:
6	chr2:20091934..20093841-chr2:20217101..20219993,2	K562	blood:
7	chr2:20212137..20214593-chr2:20218188..20219836,2	MCF-7	breast:
8	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000068697	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000223734	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1016317	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1016318	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs10175486	1.00[CEU][hapmap]
rs10203067	1.00[CEU][hapmap]
rs1028051	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11096633	0.94[CEU][hapmap]
rs1147110	0.94[CEU][hapmap]
rs11903882	0.82[EUR][1000 genomes]
rs12052278	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12328613	0.94[CEU][hapmap]
rs12475660	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12478941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010930	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2278528	0.94[CEU][hapmap]
rs2304589	0.94[CEU][hapmap]
rs34309262	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754907	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3754908	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs3769763	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55920955	0.80[ASN][1000 genomes]
rs60557282	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62109428	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717139	1.00[CEU][hapmap]
rs768377	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs936509	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16987297	TTC32	cis	lymphoblastoid	seeQTL
rs16987297	LOC130502	cis	multi-tissue	Pritchard
rs16987297	KLHL29	cis	parietal	SCAN
rs16987297	LAPTM4A	cis	parietal	SCAN
rs16987297	TTC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20213000-20220600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:20213000-20227200	Weak transcription	Ovary	ovary
3	chr2:20213200-20225000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:20213200-20227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:20213200-20227000	Weak transcription	Aorta	Aorta
6	chr2:20213400-20227400	Weak transcription	Fetal Kidney	kidney
7	chr2:20213400-20232200	Weak transcription	Right Ventricle	heart
8	chr2:20213600-20227000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:20214800-20220200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:20216400-20227800	Weak transcription	Fetal Intestine Large	intestine
11	chr2:20216400-20228800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:20216600-20220400	Weak transcription	HepG2	liver
13	chr2:20216800-20224800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:20217400-20220400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:20218600-20219400	Enhancers	Left Ventricle	heart
16	chr2:20219000-20219400	Enhancers	Stomach Smooth Muscle	stomach

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