Variant report

Variant	rs2377023
Chromosome Location	chr1:226390758-226390759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226381844..226383704-chr1:226388767..226391122,2	MCF-7	breast:
2	chr1:226308697..226313328-chr1:226386714..226391667,5	K562	blood:
3	chr1:226309070..226311740-chr1:226388089..226391667,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127970	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10799339	0.81[JPT][hapmap]
rs10799344	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10799347	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap]
rs10915949	0.84[LWK][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs10915951	0.87[JPT][hapmap]
rs10915955	0.87[JPT][hapmap]
rs10915958	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140038	0.82[AMR][1000 genomes]
rs1219658	0.89[CHB][hapmap]
rs16860230	0.87[JPT][hapmap]
rs1813323	0.82[MEX][hapmap]
rs2169567	0.94[CHB][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs2254723	0.89[CHB][hapmap]
rs2377028	0.94[CHB][hapmap]
rs2615799	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2615803	0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs2666429	0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap]
rs2889536	0.80[AMR][1000 genomes]
rs2889537	0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs4638085	0.82[AMR][1000 genomes]
rs4653719	0.82[AMR][1000 genomes]
rs4653720	0.82[AMR][1000 genomes]
rs4653721	0.80[AMR][1000 genomes]
rs6605032	0.89[CHB][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs67776609	0.82[AMR][1000 genomes]
rs9724673	0.84[LWK][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs9725951	0.82[AMR][1000 genomes]
rs9729045	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2829936	chr1:226375267-226488826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2377023	GJC2	cis	cerebellum	SCAN
rs2377023	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs2377023	LIN9	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226375200-226411000	Weak transcription	Right Atrium	heart
2	chr1:226383400-226390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr1:226389000-226392000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:226389200-226391200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:226389600-226390800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:226390200-226391000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:226390200-226391000	Enhancers	GM12878-XiMat	blood
8	chr1:226390600-226391000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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