Variant report

Variant	rs6576983
Chromosome Location	chr2:97454650-97454651
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10189727	0.83[ASN][1000 genomes]
rs11682994	0.93[ASN][1000 genomes]
rs1318597	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678385	0.88[ASN][1000 genomes]
rs6576984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727384	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6730773	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68026712	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72941253	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608661	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878919	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs968470	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs994430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
10	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97430200-97462800	Weak transcription	Aorta	Aorta
2	chr2:97433000-97466800	Weak transcription	Fetal Brain Male	brain
3	chr2:97440000-97459600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:97440000-97480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:97440400-97462600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:97440400-97462800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:97440400-97462800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:97440400-97462800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:97441000-97463400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:97442600-97462800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:97442800-97462600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:97442800-97462600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:97442800-97466600	Weak transcription	Primary B cells from cord blood	blood
14	chr2:97449400-97464800	Weak transcription	GM12878-XiMat	blood
15	chr2:97449600-97462600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:97450200-97455400	Enhancers	Stomach Mucosa	stomach
17	chr2:97450600-97462800	Weak transcription	Spleen	Spleen
18	chr2:97451800-97454800	Enhancers	Fetal Intestine Large	intestine
19	chr2:97451800-97455000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:97451800-97455000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:97452000-97455000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:97452200-97454800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:97452400-97454800	Enhancers	Osteobl	bone
24	chr2:97452400-97455200	Enhancers	Esophagus	oesophagus
25	chr2:97452600-97454800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:97452600-97454800	Enhancers	HepG2	liver
27	chr2:97452800-97454800	Enhancers	Duodenum Mucosa	Duodenum
28	chr2:97453000-97462200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:97453000-97463800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:97453400-97455200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:97453600-97454800	Enhancers	Liver	Liver
32	chr2:97453600-97454800	Enhancers	HSMM	muscle
33	chr2:97453600-97455000	Enhancers	Colon Smooth Muscle	Colon
34	chr2:97453600-97455200	Enhancers	Brain Substantia Nigra	brain
35	chr2:97453600-97455400	Enhancers	Lung	lung
36	chr2:97453800-97454800	Enhancers	Brain Cingulate Gyrus	brain
37	chr2:97453800-97454800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr2:97453800-97455000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr2:97453800-97455200	Enhancers	Brain Hippocampus Middle	brain
40	chr2:97453800-97455200	Enhancers	Fetal Heart	heart
41	chr2:97453800-97455400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr2:97454000-97454800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:97454000-97454800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr2:97454000-97455000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:97454000-97455000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:97454000-97455000	Enhancers	Gastric	stomach
47	chr2:97454000-97455000	Enhancers	Pancreas	Pancrea
48	chr2:97454000-97455200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:97454000-97455200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr2:97454000-97455400	Enhancers	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links