Variant report

Variant	rs7212099
Chromosome Location	chr17:45925890-45925891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45924201..45927115-chr17:46047307..46049661,2	K562	blood:
2	chr17:45924111..45929589-chr17:45940263..45947435,9	MCF-7	breast:
3	chr17:45923698..45927608-chr17:45971618..45975136,4	K562	blood:
4	chr17:45912259..45914443-chr17:45925886..45928377,3	MCF-7	breast:
5	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
6	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
7	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10428	0.89[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs11079797	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11079799	0.82[JPT][hapmap]
rs16948424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16948662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074185	0.82[JPT][hapmap]
rs34156395	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793688	0.82[JPT][hapmap]
rs4794224	0.82[JPT][hapmap]
rs59111282	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62076102	0.90[ASN][1000 genomes]
rs62076106	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214694	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs8078688	1.00[EUR][1000 genomes]
rs916798	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9895764	1.00[EUR][1000 genomes]
rs9896712	0.86[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs9897598	1.00[EUR][1000 genomes]
rs9904503	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9915028	1.00[EUR][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7212099	ENSG00000141295	cis	multi-tissue	Pritchard
rs7212099	SCRN2	cis	lymphoblastoid	seeQTL
rs7212099	CALCOCO2	cis	cerebellum	SCAN
rs7212099	SCRN2	cis	Muscle Skeletal	GTEx
rs7212099	CNTNAP1	cis	cerebellum	SCAN
rs7212099	SCRN2	cis	Whole Blood	GTEx
rs7212099	SCRN2	cis	lung	GTEx
rs7212099	SCRN2	cis	multi-tissue	Pritchard
rs7212099	SCRN2	cis	Liver	GTEx
rs7212099	SCRN2	cis	Adipose Subcutaneous	GTEx
rs7212099	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs7212099	KRTAP4-1	cis	cerebellum	SCAN
rs7212099	SCRN2	cis	Esophagus Mucosa	GTEx
rs7212099	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs7212099	SCRN2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
2	chr17:45921000-45927200	Weak transcription	A549	lung
3	chr17:45921200-45926000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:45922600-45927600	Weak transcription	Hela-S3	cervix
5	chr17:45923800-45926000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr17:45923800-45926400	Weak transcription	K562	blood
7	chr17:45924000-45926000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr17:45924000-45926200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr17:45924200-45926200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr17:45924200-45928000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr17:45924800-45926600	Enhancers	HMEC	breast
12	chr17:45925000-45927000	Weak transcription	NHEK	skin
13	chr17:45925200-45926800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr17:45925200-45927800	Weak transcription	Gastric	stomach
15	chr17:45925400-45926000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr17:45925400-45926000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr17:45925400-45926200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:45925400-45927200	Weak transcription	Spleen	Spleen
19	chr17:45925400-45927600	Weak transcription	Pancreas	Pancrea
20	chr17:45925600-45926000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr17:45925600-45926000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr17:45925600-45926200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr17:45925600-45926400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
24	chr17:45925600-45927000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:45925800-45926000	Flanking Active TSS	Placenta	Placenta
26	chr17:45925800-45926200	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:45925800-45926200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr17:45925800-45926200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:45925800-45927800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:45925800-45927800	Weak transcription	Right Ventricle	heart
31	chr17:45925800-45928000	Weak transcription	Lung	lung

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