Variant report

Variant	rs9728310
Chromosome Location	chr1:226331772-226331773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226331675-226332080	K562	blood:	n/a	n/a
2	POLR2A	chr1:226330672-226332204	K562	blood:	n/a	n/a
3	POLR2A	chr1:226331671-226332037	GM12891	blood:	n/a	n/a
4	NR2F2	chr1:226331754-226332122	K562	blood:	n/a	n/a
5	POLR2A	chr1:226331701-226332147	GM12891	blood:	n/a	n/a
6	CEBPB	chr1:226331760-226332159	K562	blood:	n/a	n/a
7	POLR2A	chr1:226331679-226332115	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:226331707-226332097	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:226331753-226332143	HepG2	liver:	n/a	n/a
10	POLR2A	chr1:226331610-226332025	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226315099..226318031-chr1:226330803..226332605,3	MCF-7	breast:
2	chr1:226325163..226327819-chr1:226330574..226333396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234478	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10732276	0.92[EUR][1000 genomes]
rs10799337	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10799340	0.88[CEU][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10915952	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915953	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915954	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs12032630	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12047894	0.81[EUR][1000 genomes]
rs12136759	0.83[MEX][hapmap]
rs1219671	0.82[CHD][hapmap]
rs1877155	0.82[CHD][hapmap]
rs2306121	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2889539	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3914142	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4653718	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653722	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9286997	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9286998	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9659225	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9659397	0.81[AMR][1000 genomes]
rs9660696	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9660874	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9660924	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9661836	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9662709	0.90[EUR][1000 genomes]
rs9725308	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9725342	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9728014	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9729232	0.92[EUR][1000 genomes]
rs9729554	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9728310	PARP1	cis	cerebellum	SCAN
rs9728310	ACBD3	cis	normal skin	skin_eQTL
rs9728310	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226320800-226334000	Weak transcription	K562	blood
3	chr1:226321200-226331800	Weak transcription	HSMMtube	muscle
4	chr1:226321400-226331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:226321400-226333800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:226321400-226333800	Weak transcription	GM12878-XiMat	blood
7	chr1:226321800-226331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:226322000-226334400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:226322200-226331800	Weak transcription	HMEC	breast
10	chr1:226322800-226333000	Weak transcription	Brain Substantia Nigra	brain
11	chr1:226323200-226331800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:226323200-226331800	Weak transcription	Spleen	Spleen
13	chr1:226323200-226333200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:226323200-226333600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:226323200-226333800	Weak transcription	A549	lung
16	chr1:226323200-226334400	Weak transcription	NHEK	skin
17	chr1:226323200-226344600	Weak transcription	Brain Angular Gyrus	brain
18	chr1:226323400-226331800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:226323400-226331800	Weak transcription	Left Ventricle	heart
20	chr1:226323400-226338400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:226323600-226331800	Weak transcription	Liver	Liver
22	chr1:226323600-226333800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:226323600-226333800	Weak transcription	Esophagus	oesophagus
24	chr1:226323600-226334000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:226323600-226338400	Weak transcription	Fetal Kidney	kidney
26	chr1:226323600-226339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:226323600-226339800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:226323600-226346000	Weak transcription	Fetal Heart	heart
29	chr1:226323800-226331800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:226323800-226333600	Weak transcription	Fetal Intestine Large	intestine
31	chr1:226323800-226333800	Weak transcription	Ovary	ovary
32	chr1:226323800-226333800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:226323800-226334000	Weak transcription	Right Ventricle	heart
34	chr1:226323800-226338600	Weak transcription	Fetal Brain Male	brain
35	chr1:226323800-226355000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:226324000-226331800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:226324000-226331800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:226324000-226331800	Weak transcription	HepG2	liver
39	chr1:226324000-226333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:226324000-226339800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:226324000-226340000	Weak transcription	Stomach Mucosa	stomach
42	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:226324200-226331800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:226324200-226333000	Weak transcription	Colonic Mucosa	Colon
45	chr1:226324400-226334000	Weak transcription	Lung	lung
46	chr1:226324400-226334000	Weak transcription	Thymus	Thymus
47	chr1:226324400-226339800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:226324400-226346200	Weak transcription	Pancreas	Pancrea
49	chr1:226324800-226334200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:226325800-226333800	Weak transcription	Aorta	Aorta

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