Variant report

Variant	rs2413016
Chromosome Location	chr22:31458203-31458204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31450718..31452880-chr22:31457371..31459942,3	MCF-7	breast:
2	chr22:31363691..31369255-chr22:31456002..31460514,7	MCF-7	breast:
3	chr22:31457775..31462699-chr22:31474304..31478789,5	MCF-7	breast:
4	chr22:31364481..31367281-chr22:31457492..31460562,3	MCF-7	breast:
5	chr22:31451720..31453462-chr22:31457824..31459739,2	MCF-7	breast:
6	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
7	chr22:31455775..31461842-chr22:31476267..31480955,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183963	Chromatin interaction
ENSG00000273387	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000133422	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11705137	1.00[CHD][hapmap]
rs12167220	1.00[CHD][hapmap]
rs12485186	1.00[ASN][1000 genomes]
rs1990125	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017301	1.00[CHD][hapmap]
rs4820933	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56017492	1.00[ASN][1000 genomes]
rs5753431	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs5753446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5997854	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs73156781	1.00[ASN][1000 genomes]
rs73156787	1.00[ASN][1000 genomes]
rs73156792	1.00[ASN][1000 genomes]
rs73156799	0.87[ASN][1000 genomes]
rs917208	1.00[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs9621188	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv964620	chr22:31452981-31465140	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv962852	chr22:31455516-31465140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2413016	C22orf42	cis	cerebellum	SCAN
rs2413016	SLC35E4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31455400-31458400	Enhancers	K562	blood
2	chr22:31455800-31458400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr22:31456200-31460000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:31456200-31460000	Weak transcription	A549	lung
5	chr22:31456400-31458400	Weak transcription	Fetal Intestine Small	intestine
6	chr22:31456600-31461000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr22:31456800-31458800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr22:31457000-31459200	Weak transcription	HepG2	liver
9	chr22:31457000-31465400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:31457800-31459400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr22:31458200-31458400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:31458200-31458400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr22:31458200-31458400	Enhancers	Adipose Nuclei	Adipose
14	chr22:31458200-31458600	Enhancers	Fetal Muscle Trunk	muscle
15	chr22:31458200-31458600	Enhancers	Hela-S3	cervix
16	chr22:31458200-31459200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr22:31458200-31459400	Enhancers	NHEK	skin
18	chr22:31458200-31459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr22:31458200-31459600	Enhancers	HMEC	breast
20	chr22:31458200-31459800	Enhancers	Fetal Intestine Large	intestine

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