Variant report

Variant	rs1835873
Chromosome Location	chr5:57135050-57135051
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12519846	0.85[ASN][1000 genomes]
rs12654378	0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs16887464	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs16887469	0.86[ASN][1000 genomes]
rs1816391	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1821211	0.86[ASN][1000 genomes]
rs1835875	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1835876	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2053013	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2408855	0.86[ASN][1000 genomes]
rs2898030	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2898031	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898032	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34152283	0.99[ASN][1000 genomes]
rs34397458	0.86[ASN][1000 genomes]
rs34711481	0.97[ASN][1000 genomes]
rs35483666	0.86[ASN][1000 genomes]
rs4700229	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700230	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62360111	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6450440	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6450441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6868222	0.83[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs6892809	0.85[ASN][1000 genomes]
rs7701201	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7717208	0.83[ASN][1000 genomes]
rs7721249	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7722730	0.81[JPT][hapmap];0.83[ASN][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	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1835873	IL6ST	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57127400-57137400	Enhancers	NHEK	skin
2	chr5:57129200-57136800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:57130200-57136000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:57130200-57139200	Enhancers	HMEC	breast
5	chr5:57130600-57137800	Enhancers	HSMM	muscle
6	chr5:57131200-57137800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:57131400-57136800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:57131400-57137400	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:57131400-57140000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:57131400-57141000	Weak transcription	Left Ventricle	heart
11	chr5:57131600-57137200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:57131600-57137400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:57131800-57136800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:57132000-57136800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:57132000-57137800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:57132400-57137200	Weak transcription	Fetal Brain Male	brain
17	chr5:57132600-57137400	Enhancers	HUVEC	blood vessel
18	chr5:57132600-57137600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:57132800-57135800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:57132800-57137400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:57132800-57139000	Enhancers	NHDF-Ad	bronchial
22	chr5:57133000-57135600	Enhancers	NH-A	brain
23	chr5:57133000-57135800	Enhancers	Hela-S3	cervix
24	chr5:57133000-57137800	Enhancers	HSMMtube	muscle
25	chr5:57133200-57137400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:57133600-57135200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:57133800-57137600	Weak transcription	Fetal Heart	heart
28	chr5:57134000-57135200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:57134000-57135200	Enhancers	NHLF	lung
30	chr5:57134000-57135800	Enhancers	Fetal Stomach	stomach
31	chr5:57134200-57136800	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:57134200-57136800	Weak transcription	Placenta	Placenta
33	chr5:57134400-57136800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:57134400-57136800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:57134400-57137000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:57134400-57137200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:57134600-57135800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:57134800-57135600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:57135000-57135400	Enhancers	A549	lung
40	chr5:57135000-57136800	Weak transcription	Osteobl	bone
41	chr5:57135000-57137000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:57135000-57137800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links