Variant report

Variant	rs12742850
Chromosome Location	chr1:93940090-93940091
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	chr1:93921576..93924878-chr1:93939803..93941437,3	K562	blood:
2	chr1:93921576..93924345-chr1:93939803..93941370,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1055654	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10874786	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874790	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164924	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11164936	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11164938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164942	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164943	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12042552	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12044883	0.82[JPT][hapmap]
rs12123339	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12133576	0.90[JPT][hapmap]
rs12135266	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12138486	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12406245	0.90[JPT][hapmap]
rs1426318	0.90[JPT][hapmap]
rs1559828	0.90[JPT][hapmap]
rs1812668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237438	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap]
rs237439	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2391271	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2624436	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624439	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35102250	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3767964	0.90[JPT][hapmap]
rs3767966	0.82[CHB][hapmap]
rs3767967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847240	0.90[JPT][hapmap]
rs4847245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847429	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4847431	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7525248	0.90[JPT][hapmap]
rs7546702	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551016	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8179368	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12742850	TMED5	cis	cerebellum	SCAN
rs12742850	DR1	cis	multi-tissue	Pritchard
rs12742850	TMED5	cis	parietal	SCAN
rs12742850	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12742850	PIGH	trans	cerebellum	SCAN
rs12742850	NDUFA4	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93920000-93943800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:93922600-93944000	Weak transcription	Gastric	stomach
3	chr1:93927600-93943800	Weak transcription	Pancreas	Pancrea
4	chr1:93929000-93946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:93930600-93943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:93933400-93943800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:93934200-93943600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:93934200-93943800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:93937600-93943800	Weak transcription	HepG2	liver
10	chr1:93937600-93954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:93938000-93940400	Weak transcription	Adipose Nuclei	Adipose
12	chr1:93938000-93941400	Weak transcription	Liver	Liver
13	chr1:93938000-93942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:93939200-93940400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:93939200-93943600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:93939400-93940600	Enhancers	Fetal Heart	heart
17	chr1:93939600-93940400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:93939600-93942200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:93939600-93943400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:93939600-93946000	Weak transcription	Left Ventricle	heart
21	chr1:93939800-93940200	Enhancers	Fetal Lung	lung
22	chr1:93939800-93940600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:93940000-93940200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr1:93940000-93940600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:93940000-93942000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:93940000-93942400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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