Variant report

Variant	rs11098160
Chromosome Location	chr4:79291535-79291536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11098164	0.93[ASN][1000 genomes]
rs11932185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471750	0.92[ASN][1000 genomes]
rs1872264	0.90[ASN][1000 genomes]
rs1872265	0.92[ASN][1000 genomes]
rs2100483	0.97[ASN][1000 genomes]
rs4975163	0.92[ASN][1000 genomes]
rs4975164	0.89[ASN][1000 genomes]
rs6533620	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670150	0.90[ASN][1000 genomes]
rs7679527	0.92[ASN][1000 genomes]
rs923015	0.92[ASN][1000 genomes]
rs923016	0.92[ASN][1000 genomes]
rs923017	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs923019	0.90[CHB][hapmap];0.93[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	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11098160	RCHY1	cis	cerebellum	SCAN
rs11098160	RCHY1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79275400-79310600	Weak transcription	Aorta	Aorta
2	chr4:79282400-79292800	Weak transcription	Psoas Muscle	Psoas
3	chr4:79282800-79295000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:79283000-79291600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:79283600-79292400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:79283600-79292800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:79284600-79353600	Weak transcription	Left Ventricle	heart
8	chr4:79284800-79293400	Weak transcription	Fetal Intestine Large	intestine
9	chr4:79285600-79296600	Weak transcription	Fetal Stomach	stomach
10	chr4:79286800-79291800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:79288000-79318400	Weak transcription	Pancreas	Pancrea
12	chr4:79288200-79300200	Weak transcription	HSMMtube	muscle
13	chr4:79288400-79300200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:79289600-79291600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:79289600-79291800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:79289600-79292200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:79289600-79292200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr4:79289800-79291600	Weak transcription	Fetal Kidney	kidney
19	chr4:79289800-79292200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:79290000-79291800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:79290200-79291800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr4:79290200-79293000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:79290200-79310800	Weak transcription	Brain Anterior Caudate	brain
24	chr4:79290400-79297200	Strong transcription	HepG2	liver
25	chr4:79290800-79291600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:79290800-79291800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:79290800-79292600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:79291000-79291600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr4:79291000-79291600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:79291000-79291600	Strong transcription	Fetal Lung	lung
31	chr4:79291000-79291800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:79291000-79291800	Enhancers	NHDF-Ad	bronchial
33	chr4:79291000-79292000	Genic enhancers	H1 Cell Line	embryonic stem cell
34	chr4:79291000-79292000	Enhancers	Esophagus	oesophagus
35	chr4:79291000-79292200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
36	chr4:79291000-79292200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:79291000-79292400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:79291000-79295000	Weak transcription	Fetal Brain Male	brain
39	chr4:79291200-79291600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:79291200-79292000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
41	chr4:79291200-79308400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:79291200-79314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:79291400-79291600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:79291400-79291600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:79291400-79291800	Enhancers	Fetal Intestine Small	intestine

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