Variant report

Variant	rs12363628
Chromosome Location	chr11:72987038-72987039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:72986629..72988131-chr11:72989810..72992579,2	MCF-7	breast:
2	chr11:72905564..72908217-chr11:72984750..72988310,3	MCF-7	breast:
3	chr11:72985840..72987408-chr11:73017955..73020742,2	MCF-7	breast:
4	chr11:72975533..72978051-chr11:72986526..72988737,2	MCF-7	breast:
5	chr11:72897629..72900553-chr11:72986169..72988711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110237	Chromatin interaction
ENSG00000171631	Chromatin interaction
ENSG00000257038	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898913	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10898915	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235699	1.00[JPT][hapmap]
rs11235701	0.95[ASN][1000 genomes]
rs11235703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235705	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235706	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235709	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235712	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235713	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12276627	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12787775	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12790447	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12790863	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12794405	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894075	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28513476	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023835	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34385073	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35455220	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35963948	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4432047	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592517	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67897720	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103650	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106903	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114877	0.95[ASN][1000 genomes]
rs7116594	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123808	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127013	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127179	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127705	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7127940	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925649	1.00[JPT][hapmap]
rs7930891	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942649	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882904	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988805	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832208	chr11:72876184-73091003	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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	54 gene(s)	inside rSNPs	diseases
2	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12363628	PAAF1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72977200-72991600	Weak transcription	Osteobl	bone
2	chr11:72980400-72987200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:72980400-72998400	Weak transcription	Right Atrium	heart
4	chr11:72981200-72991000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr11:72983400-72994600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:72983600-72994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:72983800-72988600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:72984600-73000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:72985000-72992000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:72986200-72991600	Weak transcription	GM12878-XiMat	blood
11	chr11:72986200-72991800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:72986200-72999800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:72986400-72987200	Enhancers	Placenta	Placenta
14	chr11:72986400-72991600	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:72986600-72988000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr11:72986600-72988200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:72986600-72990800	Weak transcription	Adipose Nuclei	Adipose
18	chr11:72986800-72987200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:72986800-72987200	Enhancers	Fetal Intestine Large	intestine
20	chr11:72986800-72988000	Weak transcription	Fetal Intestine Small	intestine
21	chr11:72986800-72988400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:72986800-72988400	Weak transcription	A549	lung
23	chr11:72986800-72991400	Weak transcription	Spleen	Spleen
24	chr11:72986800-72991600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:72986800-72992200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:72986800-72992400	Weak transcription	Esophagus	oesophagus
27	chr11:72987000-72992400	Weak transcription	Placenta Amnion	Placenta Amnion

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