Variant report

Variant	rs17198955
Chromosome Location	chr2:190387243-190387244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190386851..190389164-chr2:190404426..190407067,2	K562	blood:
2	chr2:190386430..190387354-chr2:190405763..190406692,2	MCF-7	breast:
3	chr2:190380308..190383170-chr2:190385325..190387858,2	K562	blood:
4	chr2:190385297..190387397-chr2:190391167..190392889,2	K562	blood:
5	chr2:190379388..190384195-chr2:190384322..190387858,5	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10189190	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10202029	1.00[JPT][hapmap]
rs10206543	1.00[CHB][hapmap]
rs1123109	1.00[ASW][hapmap]
rs11568351	1.00[ASW][hapmap]
rs11674773	1.00[JPT][hapmap]
rs11677198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs11680808	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs11685775	1.00[JPT][hapmap]
rs11691332	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12465339	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13007486	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13018571	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13027987	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029665	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13032311	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1371468	1.00[CHB][hapmap]
rs1371469	1.00[CHB][hapmap]
rs1469967	0.91[AMR][1000 genomes]
rs17198934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17198941	1.00[CHB][hapmap]
rs17271057	1.00[ASW][hapmap]
rs17271134	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17271183	1.00[ASW][hapmap]
rs2119070	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289225	1.00[ASW][hapmap]
rs35000023	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35078179	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35209105	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35574177	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4277558	1.00[JPT][hapmap]
rs62184660	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726093	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[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
rs17198955	COL5A2	cis	parietal	SCAN
rs17198955	SLC40A1	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190380400-190391800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:190383400-190387400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:190384400-190389400	Enhancers	Liver	Liver
4	chr2:190384400-190390000	Enhancers	Fetal Intestine Large	intestine
5	chr2:190384400-190390000	Enhancers	Fetal Intestine Small	intestine
6	chr2:190384800-190393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:190385000-190387400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:190385600-190387800	Enhancers	K562	blood
9	chr2:190385800-190387600	Enhancers	Placenta	Placenta
10	chr2:190385800-190387800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr2:190385800-190388000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:190385800-190388000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:190385800-190388000	Enhancers	Small Intestine	intestine
14	chr2:190386000-190388600	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:190386000-190389200	Enhancers	Stomach Mucosa	stomach
16	chr2:190386200-190388000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr2:190386200-190388000	Enhancers	Fetal Lung	lung
18	chr2:190386400-190387800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:190386400-190387800	Flanking Active TSS	A549	lung
20	chr2:190386400-190387800	Enhancers	Hela-S3	cervix
21	chr2:190386600-190387600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:190386600-190388000	Enhancers	HSMMtube	muscle
23	chr2:190386600-190398200	Weak transcription	Aorta	Aorta
24	chr2:190386800-190387400	Weak transcription	Right Atrium	heart
25	chr2:190386800-190387600	Enhancers	HSMM	muscle
26	chr2:190386800-190388000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:190386800-190388000	Enhancers	Adipose Nuclei	Adipose
28	chr2:190386800-190389200	Weak transcription	Colonic Mucosa	Colon
29	chr2:190387000-190387400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:190387000-190387800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:190387000-190388000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:190387000-190388000	Enhancers	Ovary	ovary
33	chr2:190387200-190387400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:190387200-190387400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr2:190387200-190387600	Enhancers	Brain Hippocampus Middle	brain
36	chr2:190387200-190387600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:190387200-190387800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:190387200-190387800	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:190387200-190387800	Enhancers	Brain Substantia Nigra	brain
40	chr2:190387200-190387800	Enhancers	Psoas Muscle	Psoas
41	chr2:190387200-190387800	Flanking Active TSS	HepG2	liver
42	chr2:190387200-190388000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr2:190387200-190388000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:190387200-190388000	Enhancers	Gastric	stomach
45	chr2:190387200-190388000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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