Variant report

Variant	rs1402840
Chromosome Location	chr2:169636651-169636652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169630763..169636990-chr2:169638094..169645299,10	K562	blood:
2	chr2:169632772..169636827-chr2:169642052..169645299,4	K562	blood:

Variant related genes	Relation type
ENSG00000227617	Chromatin interaction
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12692886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017628	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs16855872	1.00[CHB][hapmap]
rs2390731	0.83[ASN][1000 genomes]
rs3845726	1.00[CHB][hapmap]
rs3845727	1.00[CHB][hapmap]
rs3856426	1.00[CHB][hapmap]
rs3914920	1.00[CHB][hapmap]
rs4233821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668101	0.83[ASN][1000 genomes]
rs4668103	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs6433088	0.83[ASN][1000 genomes]
rs6433092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558965	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7585751	0.83[ASN][1000 genomes]
rs7589456	0.83[ASN][1000 genomes]
rs8304	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402840	C2orf77	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169610800-169637400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:169622200-169641400	Weak transcription	Small Intestine	intestine
3	chr2:169626800-169641800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:169628000-169637000	Weak transcription	Hela-S3	cervix
5	chr2:169631000-169637600	Weak transcription	Brain Germinal Matrix	brain
6	chr2:169631200-169637600	Weak transcription	Fetal Heart	heart
7	chr2:169632600-169637000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:169632800-169636800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:169632800-169636800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:169632800-169637800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:169632800-169638000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:169634000-169637400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:169634200-169637600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:169634200-169643000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:169635800-169637000	Enhancers	Pancreas	Pancrea
16	chr2:169636000-169637600	Enhancers	Fetal Muscle Leg	muscle
17	chr2:169636200-169637400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:169636400-169639400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:169636600-169637400	Weak transcription	Lung	lung
20	chr2:169636600-169637800	Enhancers	A549	lung
21	chr2:169636600-169638000	Enhancers	Fetal Lung	lung
22	chr2:169636600-169638200	Enhancers	HepG2	liver
23	chr2:169636600-169638800	Enhancers	Fetal Kidney	kidney

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