Variant report

Variant	rs9642972
Chromosome Location	chr8:102604306-102604307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:102503587..102506004-chr8:102600065..102605597,5	MCF-7	breast:
2	chr8:102503060..102507030-chr8:102601716..102605768,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083307	Chromatin interaction
ENSG00000254024	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10095480	0.91[CEU][hapmap]
rs12678441	0.84[CEU][hapmap]
rs1404949	0.84[CEU][hapmap]
rs1573279	0.84[CEU][hapmap]
rs1573280	0.84[CEU][hapmap]
rs1573281	0.87[CEU][hapmap]
rs1573282	0.83[CEU][hapmap]
rs1573283	0.83[CEU][hapmap]
rs16867971	0.92[CEU][hapmap]
rs2030783	0.84[CEU][hapmap]
rs2030784	0.84[CEU][hapmap]
rs2030785	0.84[CEU][hapmap]
rs2030786	0.88[CEU][hapmap]
rs2211918	0.84[CEU][hapmap]
rs2507794	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2507795	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4236766	0.84[CEU][hapmap]
rs4392865	0.84[CEU][hapmap]
rs4588817	0.83[CEU][hapmap]
rs4734027	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4734544	0.84[CEU][hapmap]
rs4734545	0.83[CEU][hapmap]
rs4734546	0.84[CEU][hapmap]
rs4734551	0.84[CEU][hapmap]
rs4734553	0.84[CEU][hapmap]
rs4734559	0.84[CEU][hapmap]
rs4734560	0.84[CEU][hapmap]
rs503895	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs567029	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579505	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468780	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6468781	0.83[AMR][1000 genomes]
rs6468782	0.84[CEU][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs7462010	0.84[CEU][hapmap]
rs7820410	0.84[CEU][hapmap]
rs7820809	0.84[CEU][hapmap]
rs7823289	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7824065	0.84[CEU][hapmap]
rs7835187	0.83[CEU][hapmap]
rs7838983	0.82[CEU][hapmap]
rs9649995	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891230	chr8:102569309-102604306	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv396957	chr8:102598319-102604328	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3361711	chr8:102604246-102604684	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9642972	PABPC1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102552200-102620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:102590600-102631600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr8:102590600-102635200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:102592000-102611000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr8:102594000-102611600	Weak transcription	Fetal Intestine Large	intestine
6	chr8:102594200-102612000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:102595800-102605400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:102596000-102615000	Weak transcription	Stomach Mucosa	stomach
9	chr8:102597400-102606600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:102597400-102616000	Weak transcription	Gastric	stomach
11	chr8:102597400-102620600	Weak transcription	Colonic Mucosa	Colon
12	chr8:102599000-102611600	Weak transcription	Pancreas	Pancrea
13	chr8:102600600-102619200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr8:102601400-102612200	Weak transcription	Fetal Stomach	stomach
15	chr8:102601600-102611600	Weak transcription	Fetal Intestine Small	intestine
16	chr8:102601600-102616200	Weak transcription	Fetal Kidney	kidney
17	chr8:102602200-102608600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:102602400-102611200	Weak transcription	HMEC	breast
19	chr8:102602800-102611600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr8:102603000-102606200	Weak transcription	NHEK	skin
21	chr8:102603400-102607600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:102603600-102606800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr8:102603600-102607000	Strong transcription	Placenta	Placenta
24	chr8:102603800-102607000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:102603800-102607000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr8:102603800-102607400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr8:102603800-102607600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr8:102604000-102606600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr8:102604000-102607000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:102604000-102612000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr8:102604000-102614600	Weak transcription	Fetal Lung	lung
32	chr8:102604200-102605000	Strong transcription	Esophagus	oesophagus
33	chr8:102604200-102605800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr8:102604200-102612000	Weak transcription	Rectal Mucosa Donor 31	rectum

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