Variant report

Variant	rs1920650
Chromosome Location	chr3:160335588-160335589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160334651..160337629-chr3:160364585..160366181,2	MCF-7	breast:
2	chr3:160334213..160336560-chr3:160410896..160413841,2	MCF-7	breast:
3	chr3:160329547..160332346-chr3:160334349..160336341,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10460866	0.85[ASN][1000 genomes]
rs10923	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10936203	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11709232	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs11711627	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712392	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713230	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11721112	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12639488	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13062928	0.80[ASN][1000 genomes]
rs13065269	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074231	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075424	0.91[ASN][1000 genomes]
rs13085507	0.80[ASN][1000 genomes]
rs1403045	0.83[CEU][hapmap]
rs16831337	0.84[CEU][hapmap]
rs17236494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17826257	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1879797	0.83[CEU][hapmap]
rs1882125	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1920649	0.83[AFR][1000 genomes]
rs1920652	0.82[AFR][1000 genomes]
rs1920663	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2141668	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178451	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35008770	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498840	0.84[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs3732706	0.81[JPT][hapmap]
rs3851365	0.81[JPT][hapmap]
rs4133253	0.84[CEU][hapmap]
rs4679903	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679904	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57718211	0.80[ASN][1000 genomes]
rs6806755	0.84[CEU][hapmap]
rs71314011	0.85[ASN][1000 genomes]
rs7610939	0.84[CEU][hapmap]
rs7633839	0.84[CEU][hapmap]
rs7634255	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7644186	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9816525	0.83[AFR][1000 genomes]
rs9822982	0.81[AFR][1000 genomes]
rs9857106	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1920650	IFT80	cis	cerebellum	SCAN
rs1920650	KLRB1	trans	parietal	SCAN
rs1920650	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs1920650	IFT80	cis	parietal	SCAN
rs1920650	TMEM212	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160333600-160336200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:160333800-160335600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:160334000-160336200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:160334200-160335600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:160334200-160335600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:160334200-160336400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:160334200-160336400	Enhancers	Pancreas	Pancrea
8	chr3:160334200-160336400	Enhancers	Psoas Muscle	Psoas
9	chr3:160334200-160336400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:160334200-160336400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:160334400-160335800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:160334800-160335600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:160335000-160336200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160335000-160336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:160335000-160336200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:160335200-160336200	Enhancers	Fetal Intestine Large	intestine
17	chr3:160335200-160336200	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:160335400-160335600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:160335400-160335600	Flanking Active TSS	Liver	Liver
20	chr3:160335400-160335800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:160335400-160336200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:160335400-160336200	Enhancers	Stomach Mucosa	stomach
23	chr3:160335400-160336400	Weak transcription	HMEC	breast

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