Variant report

Variant	rs17320040
Chromosome Location	chr3:112968917-112968918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1499898	1.00[ASN][1000 genomes]
rs16845106	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860709	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860720	1.00[ASN][1000 genomes]
rs16860770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17255950	1.00[AFR][1000 genomes]
rs17256551	1.00[AFR][1000 genomes]
rs17256752	1.00[AFR][1000 genomes]
rs17320242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17322613	1.00[AFR][1000 genomes]
rs2291412	1.00[AFR][1000 genomes]
rs2399476	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34600669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41271353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56772417	1.00[AFR][1000 genomes]
rs57104308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57115529	1.00[AFR][1000 genomes]
rs57164268	1.00[AFR][1000 genomes]
rs58905600	1.00[AFR][1000 genomes]
rs58988763	1.00[AFR][1000 genomes]
rs59493419	1.00[AFR][1000 genomes]
rs59590258	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59742486	1.00[AFR][1000 genomes]
rs60070011	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60582065	1.00[AFR][1000 genomes]
rs60697865	1.00[AFR][1000 genomes]
rs60940543	1.00[AFR][1000 genomes]
rs61035513	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61594119	1.00[AFR][1000 genomes]
rs735	1.00[AFR][1000 genomes]
rs9820139	0.95[ASN][1000 genomes]
rs9832953	0.93[ASN][1000 genomes]
rs9849714	1.00[ASN][1000 genomes]
rs9855011	1.00[ASN][1000 genomes]
rs9872998	0.95[ASN][1000 genomes]
rs9878424	0.95[ASN][1000 genomes]
rs998647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs999365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112958600-112969000	Weak transcription	Spleen	Spleen
3	chr3:112961400-112969400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:112962400-112969000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:112962800-112972400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:112963000-112969200	Weak transcription	Pancreas	Pancrea
8	chr3:112963000-112972800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:112964000-112969000	Enhancers	HSMM	muscle
10	chr3:112964200-112969400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:112964600-112971400	Enhancers	HSMMtube	muscle
12	chr3:112965800-112969800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:112966200-112972400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:112966400-112969800	Enhancers	HMEC	breast
15	chr3:112966800-112969000	Enhancers	NH-A	brain
16	chr3:112966800-112969600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:112966800-112972600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:112966800-112973600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:112967000-112972400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:112967200-112969000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:112967200-112969400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:112967200-112972200	Weak transcription	Fetal Thymus	thymus
23	chr3:112967200-112973200	Weak transcription	Colonic Mucosa	Colon
24	chr3:112967200-112973200	Weak transcription	Right Atrium	heart
25	chr3:112967400-112969200	Enhancers	Osteobl	bone
26	chr3:112967400-112969400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:112967400-112972600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:112967400-112972600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:112967400-112972600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:112968000-112969000	Enhancers	NHDF-Ad	bronchial
31	chr3:112968000-112969000	Enhancers	NHEK	skin
32	chr3:112968000-112970200	Strong transcription	Gastric	stomach
33	chr3:112968000-112971400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:112968000-112973200	Weak transcription	Left Ventricle	heart
35	chr3:112968200-112969000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:112968200-112969200	Weak transcription	Esophagus	oesophagus
37	chr3:112968200-112969200	Genic enhancers	Stomach Smooth Muscle	stomach
38	chr3:112968200-112969400	Weak transcription	Fetal Brain Female	brain
39	chr3:112968200-112969800	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr3:112968200-112969800	Weak transcription	Lung	lung
41	chr3:112968200-112970000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:112968200-112970200	Genic enhancers	Fetal Muscle Leg	muscle
43	chr3:112968200-112972400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:112968200-112972400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:112968200-112972400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:112968400-112969000	Weak transcription	Brain Substantia Nigra	brain
47	chr3:112968400-112969200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:112968400-112971400	Strong transcription	Fetal Stomach	stomach
49	chr3:112968400-112972400	Weak transcription	Fetal Brain Male	brain
50	chr3:112968400-112973000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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