Variant report

Variant	rs11172071
Chromosome Location	chr12:57331271-57331272
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57330845..57332526-chr12:57336068..57338551,2	MCF-7	breast:
2	chr12:57323485..57328382-chr12:57328704..57333004,6	K562	blood:
3	chr12:57322265..57324003-chr12:57330480..57332983,2	MCF-7	breast:
4	chr12:57319668..57321739-chr12:57328699..57331375,2	MCF-7	breast:
5	chr12:57328529..57331302-chr12:57397442..57399597,2	K562	blood:
6	chr12:57325326..57326887-chr12:57330449..57332916,2	K562	blood:

Variant related genes	Relation type
ENSG00000170426	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10506347	0.85[GIH][hapmap]
rs10506350	0.85[GIH][hapmap]
rs1072669	0.94[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876960	0.94[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172072	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172076	0.87[EUR][1000 genomes]
rs12810024	0.85[GIH][hapmap]
rs1601405	0.89[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17119301	0.82[GIH][hapmap]
rs1825514	0.88[ASW][hapmap];0.83[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1872436	0.82[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs2629413	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3782331	0.94[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57926126	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58009868	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59665366	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60101051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7136770	0.82[GIH][hapmap]
rs719749	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs719750	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7314151	0.94[CEU][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7314262	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970701	0.84[JPT][hapmap]
rs840160	0.82[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs840162	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs840163	0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs863459	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs864541	0.81[ASN][1000 genomes]
rs901069	0.94[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic 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 lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv1043846	chr12:57323709-57377509	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv12940	chr12:57331182-57379580	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11172071	NCKAP1L	cis	parietal	SCAN
rs11172071	ARHGEF25	cis	cerebellum	SCAN
rs11172071	KRT75	cis	cerebellum	SCAN
rs11172071	MYL6	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57325800-57335200	Weak transcription	Fetal Intestine Large	intestine
2	chr12:57326400-57335200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:57327000-57335200	Weak transcription	Spleen	Spleen
4	chr12:57328200-57335000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:57329400-57335200	Weak transcription	A549	lung
6	chr12:57329800-57335000	Weak transcription	NHEK	skin
7	chr12:57330000-57334600	Weak transcription	HMEC	breast
8	chr12:57330000-57335200	Weak transcription	K562	blood
9	chr12:57330200-57335200	Weak transcription	Esophagus	oesophagus

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