Variant report

Variant	rs420644
Chromosome Location	chr12:59916767-59916768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59914091..59917711-chr12:59989940..59992108,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118596	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10506395	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs10732745	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10735880	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs10735881	0.80[EUR][1000 genomes]
rs10747847	0.82[EUR][1000 genomes]
rs10747848	0.82[EUR][1000 genomes]
rs10747850	0.94[CEU][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs10747851	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs10747852	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs10783988	0.80[EUR][1000 genomes]
rs10877315	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs11173090	0.80[EUR][1000 genomes]
rs1391130	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs1497470	0.80[EUR][1000 genomes]
rs1966281	0.82[EUR][1000 genomes]
rs2132871	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132873	0.80[EUR][1000 genomes]
rs2646311	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2671854	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs275999	0.89[CEU][hapmap];0.89[CHD][hapmap]
rs276006	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs276008	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106580	0.81[EUR][1000 genomes]
rs35986083	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4019983	0.80[EUR][1000 genomes]
rs4421780	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4635118	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760291	0.82[EUR][1000 genomes]
rs4760293	0.80[EUR][1000 genomes]
rs6581255	0.82[EUR][1000 genomes]
rs6581256	0.82[EUR][1000 genomes]
rs6581257	0.95[CEU][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs6581258	0.82[EUR][1000 genomes]
rs6581259	0.82[EUR][1000 genomes]
rs6581260	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs6581261	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs7133515	0.95[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs7133612	0.95[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs7303302	0.80[EUR][1000 genomes]
rs7312134	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs7973601	0.89[ASN][1000 genomes]
rs7975216	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899129	chr12:59820966-59941423	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv469413	chr12:59856161-59916767	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv899130	chr12:59895548-59970631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv559055	chr12:59904383-59916767	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1846651	chr12:59909653-59946206	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	esv3434364	chr12:59916514-59916929	Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1826200	chr12:59916767-59946206	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1831161	chr12:59916767-59969435	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1827166	chr12:59916767-59971821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs420644	PIP4K2C	cis	parietal	SCAN
rs420644	DNAJC14	cis	parietal	SCAN
rs420644	NXPH4	cis	parietal	SCAN
rs420644	DTX3	cis	cerebellum	SCAN
rs420644	ORMDL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59912400-59921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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