Variant report

Variant	rs2359861
Chromosome Location	chr3:54676642-54676643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12497334	0.83[MEX][hapmap]
rs13084347	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs1520575	0.86[CEU][hapmap];0.89[MEX][hapmap]
rs17815840	0.89[MEX][hapmap]
rs4541376	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71301895	0.83[AMR][1000 genomes]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2359861	NISCH	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54674200-54676800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:54674200-54676800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:54674200-54677000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:54674200-54677000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:54674200-54677400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:54674400-54677800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:54674400-54678000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:54675000-54677200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:54675600-54677200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:54676000-54677200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:54676000-54677200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:54676200-54678000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:54676400-54677800	Enhancers	H9 Cell Line	embryonic stem cell
15	chr3:54676400-54679000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr3:54676600-54676800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:54676600-54676800	Enhancers	Esophagus	oesophagus
18	chr3:54676600-54677000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:54676600-54677200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:54676600-54677400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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