Variant report

Variant	rs17271134
Chromosome Location	chr2:190389803-190389804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10189190	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10202029	1.00[JPT][hapmap]
rs10206543	1.00[CHB][hapmap]
rs11674773	1.00[JPT][hapmap]
rs11677198	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11677494	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11680808	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11682165	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11685775	1.00[JPT][hapmap]
rs11691332	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694976	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12465339	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13007486	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13018571	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13027987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13029665	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13032311	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1371468	1.00[CHB][hapmap]
rs1371469	1.00[CHB][hapmap]
rs1469967	0.89[AMR][1000 genomes]
rs17198934	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17198941	1.00[CHB][hapmap]
rs17198955	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119070	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35000023	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35078179	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35209105	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35574177	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4277558	1.00[JPT][hapmap]
rs62184660	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726093	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17271134	SLC40A1	cis	cerebellum	SCAN
rs17271134	COL5A2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190380400-190391800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:190384400-190390000	Enhancers	Fetal Intestine Large	intestine
3	chr2:190384400-190390000	Enhancers	Fetal Intestine Small	intestine
4	chr2:190384800-190393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:190386600-190398200	Weak transcription	Aorta	Aorta
6	chr2:190387600-190391800	Weak transcription	HSMM	muscle
7	chr2:190387600-190392000	Weak transcription	Pancreas	Pancrea
8	chr2:190387600-190393400	Weak transcription	Right Atrium	heart
9	chr2:190387600-190397000	Weak transcription	Placenta	Placenta
10	chr2:190387800-190391400	Weak transcription	Fetal Kidney	kidney
11	chr2:190387800-190391600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:190387800-190391800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:190387800-190392000	Weak transcription	Brain Substantia Nigra	brain
14	chr2:190387800-190392000	Weak transcription	Fetal Heart	heart
15	chr2:190388000-190390000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr2:190388000-190391400	Weak transcription	Adipose Nuclei	Adipose
17	chr2:190388000-190391400	Weak transcription	Fetal Lung	lung
18	chr2:190388000-190391600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:190388000-190391600	Weak transcription	Ovary	ovary
20	chr2:190388000-190391800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:190388000-190391800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:190388000-190391800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:190388000-190392000	Weak transcription	HSMMtube	muscle
24	chr2:190388200-190391800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:190388200-190391800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:190388400-190391600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:190388400-190393000	Weak transcription	A549	lung
28	chr2:190389200-190392000	Weak transcription	Stomach Mucosa	stomach
29	chr2:190389400-190391600	Weak transcription	Liver	Liver
30	chr2:190389600-190391400	Weak transcription	Colonic Mucosa	Colon
31	chr2:190389600-190392000	Weak transcription	Small Intestine	intestine
32	chr2:190389800-190390200	Enhancers	Duodenum Mucosa	Duodenum
33	chr2:190389800-190392000	Weak transcription	HepG2	liver

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