Variant report

Variant	rs12506899
Chromosome Location	chr4:74319283-74319284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10001225	0.85[ASN][1000 genomes]
rs10002756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022167	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs10031441	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12504308	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510174	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12649712	0.96[CEU][hapmap]
rs13114289	0.80[EUR][1000 genomes]
rs13138734	0.89[CEU][hapmap]
rs13150293	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1475934	0.96[CEU][hapmap]
rs16849341	0.92[CEU][hapmap]
rs16849384	1.00[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2051512	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs2070849	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2276937	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2298839	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28532518	0.81[EUR][1000 genomes]
rs3756066	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs3775485	0.92[CEU][hapmap]
rs3775486	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs3796676	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs3796677	0.81[EUR][1000 genomes]
rs3796678	0.81[EUR][1000 genomes]
rs3822100	1.00[JPT][hapmap]
rs4018	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4024	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs4403016	0.96[CEU][hapmap]
rs4446279	1.00[JPT][hapmap]
rs4513532	0.92[CEU][hapmap]
rs4575963	0.92[CEU][hapmap]
rs4640638	1.00[JPT][hapmap]
rs4694613	0.92[CEU][hapmap]
rs6446931	0.92[CEU][hapmap]
rs6820167	0.88[CEU][hapmap]
rs6834059	1.00[JPT][hapmap]
rs6850155	0.89[CEU][hapmap]
rs6853164	0.88[CEU][hapmap]
rs714825	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs737241	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660680	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7668327	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7688274	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs9996318	0.92[CEU][hapmap];0.84[TSI][hapmap]

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	esv3430875	chr4:74243646-74420354	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Tumor biomarkers	23300138	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12506899	CCNG2	cis	cerebellum	SCAN
rs12506899	ALB	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74315200-74319600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr4:74315400-74319600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:74315400-74320200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr4:74316000-74319400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr4:74316400-74319600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:74317200-74319400	Enhancers	Small Intestine	intestine
7	chr4:74317200-74319800	Enhancers	Fetal Intestine Large	intestine
8	chr4:74317600-74321400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr4:74318000-74319600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr4:74318000-74320800	Enhancers	Fetal Intestine Small	intestine
11	chr4:74318200-74319400	Genic enhancers	HepG2	liver
12	chr4:74318200-74319600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:74318200-74319600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:74318200-74319600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr4:74318200-74319600	Enhancers	Duodenum Mucosa	Duodenum
16	chr4:74318400-74319400	Enhancers	K562	blood
17	chr4:74318400-74319600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:74318400-74319600	Enhancers	Colonic Mucosa	Colon
19	chr4:74318400-74319600	Enhancers	NHEK	skin
20	chr4:74318600-74319600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr4:74318800-74319400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:74318800-74319400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:74318800-74319400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:74318800-74319600	Flanking Active TSS	Liver	Liver
25	chr4:74318800-74319600	Enhancers	Stomach Mucosa	stomach
26	chr4:74319000-74319400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr4:74319000-74319400	Enhancers	Aorta	Aorta
28	chr4:74319000-74319400	Enhancers	Ovary	ovary
29	chr4:74319000-74319400	Enhancers	Pancreas	Pancrea
30	chr4:74319000-74319400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr4:74319000-74319400	Bivalent Enhancer	Right Atrium	heart
32	chr4:74319000-74319600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr4:74319200-74319400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:74319200-74319400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:74319200-74319600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:74319200-74319600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:74319200-74319600	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr4:74319200-74319800	Enhancers	Rectal Mucosa Donor 31	rectum

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