Variant report

Variant	rs3767966
Chromosome Location	chr1:93997477-93997478
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11164938	0.82[CHB][hapmap]
rs11164939	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164941	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12034656	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12742850	0.82[CHB][hapmap]
rs17109958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17110058	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812668	0.82[CHB][hapmap]
rs237438	0.90[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs237439	0.84[ASN][1000 genomes]
rs2433279	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2624436	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3767967	0.82[CHB][hapmap]
rs4847245	0.82[CHB][hapmap]
rs4847428	0.82[CHB][hapmap]
rs4847431	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs61780647	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61784068	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543847	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs810027	0.90[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011853	chr1:93966450-94039005	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3767966	LRRC8D	cis	parietal	SCAN
rs3767966	ARHGAP29	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93964600-94015200	Weak transcription	Fetal Brain Male	brain
2	chr1:93965000-94013200	Weak transcription	Adipose Nuclei	Adipose
3	chr1:93965000-94017400	Weak transcription	Stomach Mucosa	stomach
4	chr1:93973200-94016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:93973400-94032000	Weak transcription	Esophagus	oesophagus
6	chr1:93975400-94006400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:93984000-93997800	Weak transcription	Aorta	Aorta
8	chr1:93984200-94017400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:93984800-94016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:93985200-93998400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:93985200-94012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:93985600-94012000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:93985600-94014200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:93985600-94014200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:93985600-94017600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:93985800-94015200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:93985800-94017800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:93986000-94003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:93986000-94013600	Weak transcription	Hela-S3	cervix
20	chr1:93986000-94017600	Weak transcription	NHEK	skin
21	chr1:93986200-94004400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:93986600-94006600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:93987000-94015200	Weak transcription	Ovary	ovary
24	chr1:93987600-94000400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:93988600-93999000	Weak transcription	Psoas Muscle	Psoas
26	chr1:93989000-94012200	Weak transcription	Dnd41	blood
27	chr1:93990000-94009800	Weak transcription	Fetal Kidney	kidney
28	chr1:93990800-94003200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:93991200-94006400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:93991400-94002800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:93992000-94002800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:93992000-94014200	Weak transcription	Pancreas	Pancrea
33	chr1:93992000-94018000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:93992200-94013000	Weak transcription	HMEC	breast
35	chr1:93992200-94013800	Weak transcription	Left Ventricle	heart
36	chr1:93992200-94017800	Weak transcription	Gastric	stomach
37	chr1:93992200-94018400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:93993400-94014200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:93993800-94003800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:93994000-94012800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:93994200-93998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:93994200-94013200	Weak transcription	Placenta	Placenta
43	chr1:93994400-94000400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:93994400-94002600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:93995000-93999200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:93995000-94045000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:93995200-93997800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:93995200-93998800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:93995600-93997600	Strong transcription	HepG2	liver
50	chr1:93995600-93997600	Strong transcription	HUVEC	blood vessel

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