Variant report

Variant	rs17012072
Chromosome Location	chr4:87704969-87704970
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10012566	0.83[ASN][1000 genomes]
rs10050311	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs1035191	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs10516778	0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11561681	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11930396	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12171458	0.85[ASN][1000 genomes]
rs12510802	0.82[ASN][1000 genomes]
rs13113689	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1420621	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs17420607	0.86[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17420966	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17454154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17454662	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17694112	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17751557	0.85[CEU][hapmap]
rs2006842	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2054592	0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2054593	0.84[JPT][hapmap]
rs2230600	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2287147	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775236	0.85[JPT][hapmap]
rs3775238	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3775239	0.84[JPT][hapmap]
rs4263359	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4693150	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4693152	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4693780	0.80[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs4693784	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55670248	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57954319	0.88[ASN][1000 genomes]
rs67867077	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72665791	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72665795	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7688019	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9307026	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs969734	0.86[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87639400-87739200	Weak transcription	A549	lung
4	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
8	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
9	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
12	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
13	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:87671800-87713000	Weak transcription	HSMMtube	muscle
15	chr4:87672000-87712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:87672800-87710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:87672800-87712000	Weak transcription	Lung	lung
18	chr4:87677000-87711400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:87677200-87708600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:87679000-87712000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:87679000-87712400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:87681000-87710200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:87684400-87710000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:87686200-87712200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:87688600-87708000	Weak transcription	Fetal Stomach	stomach
26	chr4:87689400-87738200	Weak transcription	Gastric	stomach
27	chr4:87690000-87738800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:87690800-87736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:87691400-87712000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:87691600-87708400	Weak transcription	Left Ventricle	heart
31	chr4:87692800-87708000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:87692800-87734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:87693000-87706800	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:87693000-87712000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:87693000-87712200	Weak transcription	Fetal Brain Female	brain
36	chr4:87693600-87710000	Weak transcription	Ovary	ovary
37	chr4:87693800-87706600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:87693800-87708000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:87694400-87724800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:87694400-87725200	Weak transcription	NH-A	brain
41	chr4:87694400-87735600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:87695200-87711400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:87695600-87728600	Weak transcription	Adipose Nuclei	Adipose
44	chr4:87696800-87733600	Weak transcription	NHLF	lung
45	chr4:87698200-87706400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:87698200-87706800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:87698200-87707400	Weak transcription	Brain Anterior Caudate	brain
48	chr4:87698200-87710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:87698200-87728600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:87698400-87710400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links