Variant report

Variant	rs1868992
Chromosome Location	chr1:149908108-149908109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10494260	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs11205309	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11205310	0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12022928	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs12023231	0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap]
rs12023748	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12026500	0.90[ASN][1000 genomes]
rs12082689	0.84[ASN][1000 genomes]
rs12409885	0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap]
rs3738320	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs3767627	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs3767628	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3936952	0.83[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs4926386	0.83[GIH][hapmap]
rs4926400	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6660842	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72692821	0.91[ASN][1000 genomes]
rs72692823	0.85[ASN][1000 genomes]
rs7551741	0.90[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	nsv432820	chr1:148921404-149920927	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	784 gene(s)	inside rSNPs	diseases
2	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1868992	SCNM1	cis	parietal	SCAN
rs1868992	GJA8	cis	parietal	SCAN
rs1868992	MRPS21	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149900400-149908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:149900600-149908200	Weak transcription	Right Ventricle	heart
3	chr1:149900600-149908400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:149900800-149908200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:149901200-149909000	Weak transcription	GM12878-XiMat	blood
6	chr1:149901600-149908200	Weak transcription	Fetal Thymus	thymus
7	chr1:149904200-149908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:149906200-149908400	Weak transcription	Gastric	stomach
9	chr1:149906400-149912000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:149906600-149909000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:149907000-149908400	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr1:149907000-149908800	Active TSS	Fetal Intestine Large	intestine
13	chr1:149907200-149908200	Flanking Active TSS	Colon Smooth Muscle	Colon
14	chr1:149907200-149908800	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr1:149907400-149908200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:149907400-149908200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:149907400-149908200	Flanking Active TSS	Fetal Lung	lung
18	chr1:149907400-149908200	Flanking Active TSS	Rectal Smooth Muscle	rectum
19	chr1:149907400-149908200	Flanking Active TSS	NHLF	lung
20	chr1:149907400-149908400	Enhancers	Spleen	Spleen
21	chr1:149907400-149908600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:149907400-149908800	Active TSS	Small Intestine	intestine
23	chr1:149907400-149909000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:149907400-149909400	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr1:149907600-149908200	Flanking Active TSS	Fetal Kidney	kidney
26	chr1:149907600-149908200	Enhancers	K562	blood
27	chr1:149907600-149908600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:149907600-149908600	Active TSS	Fetal Brain Male	brain
29	chr1:149907600-149908800	Active TSS	NHDF-Ad	bronchial
30	chr1:149907600-149909200	Active TSS	Colonic Mucosa	Colon
31	chr1:149907600-149909400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr1:149907600-149909400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr1:149907600-149909400	Active TSS	Fetal Brain Female	brain
34	chr1:149907600-149909400	Flanking Active TSS	HepG2	liver
35	chr1:149907800-149908200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:149907800-149908200	Active TSS	Brain Germinal Matrix	brain
37	chr1:149907800-149908200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr1:149907800-149908200	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr1:149907800-149908200	Flanking Active TSS	Fetal Stomach	stomach
40	chr1:149907800-149908200	Enhancers	Pancreas	Pancrea
41	chr1:149907800-149908400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:149907800-149908400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:149907800-149908400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:149907800-149908400	Enhancers	Fetal Heart	heart
45	chr1:149907800-149908400	Flanking Active TSS	Placenta	Placenta
46	chr1:149907800-149908400	Flanking Active TSS	Ovary	ovary
47	chr1:149907800-149908400	Flanking Active TSS	NHEK	skin
48	chr1:149907800-149908600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:149907800-149908800	Flanking Active TSS	Liver	Liver
50	chr1:149907800-149908800	Active TSS	Right Atrium	heart

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