Variant report

Variant	rs17863787
Chromosome Location	chr2:234611094-234611095
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234609669..234612575-chr2:234763308..234766192,2	MCF-7	breast:
2	chr2:234604730..234606945-chr2:234609647..234612272,2	K562	blood:
3	chr2:234398388..234400630-chr2:234610958..234612928,2	MCF-7	breast:
4	chr2:234610804..234613588-chr2:234613696..234615763,4	MCF-7	breast:
5	chr2:234393470..234398510-chr2:234607909..234611299,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10167119	0.81[GIH][hapmap]
rs10168416	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10173355	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10180090	0.95[ASN][1000 genomes]
rs10197460	0.81[GIH][hapmap]
rs10202865	0.95[CEU][hapmap]
rs10929302	0.85[CEU][hapmap]
rs1105879	0.82[CEU][hapmap]
rs1105880	0.82[CEU][hapmap]
rs11695484	0.85[CEU][hapmap]
rs13009407	0.81[CEU][hapmap]
rs17862875	0.85[CEU][hapmap];0.87[YRI][hapmap]
rs17864701	0.82[CEU][hapmap]
rs1875263	0.89[GIH][hapmap]
rs2070959	1.00[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2602376	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs2741044	0.85[CEU][hapmap]
rs2741045	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs2741046	0.85[CEU][hapmap]
rs28899170	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs4148324	0.95[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4148325	0.95[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6714634	0.85[CEU][hapmap]
rs6722076	0.90[CEU][hapmap]
rs6725478	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6742078	0.95[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6744284	0.90[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs7567229	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583278	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7586110	0.81[GIH][hapmap]
rs887829	0.95[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs929596	0.81[CEU][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17863787	NPPC	cis	parietal	SCAN
rs17863787	EFHD1	cis	parietal	SCAN
rs17863787	EFHD1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234602800-234614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:234609000-234614400	Weak transcription	Stomach Mucosa	stomach
3	chr2:234609000-234614800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:234609200-234611400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:234609200-234614000	Weak transcription	NHEK	skin
6	chr2:234609200-234614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:234610600-234611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:234610800-234611600	Enhancers	Hela-S3	cervix
9	chr2:234610800-234612200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:234610800-234613200	ZNF genes & repeats	A549	lung
11	chr2:234611000-234611400	Enhancers	HUVEC	blood vessel
12	chr2:234611000-234616000	Enhancers	Liver	Liver

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