Variant report

Variant	rs10739393
Chromosome Location	chr9:116353362-116353363
allele	C/T
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	CHD1	chr9:116353115-116354700	IMR90	lung:	n/a	n/a
2	POLR2A	chr9:116352637-116354862	GM12878	blood:	n/a	n/a
3	FOXA2	chr9:116353313-116353857	A549	lung:	n/a	chr9:116353548-116353560
4	SMC3	chr9:116353269-116354822	SK-N-SH	brain:	n/a	chr9:116353518-116353525
5	POLR2A	chr9:116352831-116354938	GM12878	blood:	n/a	n/a
6	CTCF	chr9:116353300-116353450	GM12865	blood:	n/a	n/a
7	CTCF	chr9:116353300-116353450	GM12868	blood:	n/a	n/a
8	RAD21	chr9:116353349-116354925	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr9:116353334-116354701	U87	brain:	n/a	n/a
10	POLR2A	chr9:116353333-116353443	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:116352866-116354661	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116207047..116208670-chr9:116352581..116354236,2	MCF-7	breast:
2	chr9:116208228..116208821-chr9:116353155..116354195,4	MCF-7	breast:
3	chr9:116352994..116354643-chr9:116419596..116420916,16	K562	blood:
4	chr9:116171876..116174337-chr9:116351480..116354219,2	MCF-7	breast:
5	chr9:116171469..116174533-chr9:116350690..116354091,5	MCF-7	breast:

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000237073	TF binding region
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10733605	0.82[MEX][hapmap]
rs10981836	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12350531	0.85[JPT][hapmap]
rs12685417	0.92[JPT][hapmap]
rs12686023	0.92[JPT][hapmap]
rs14419	0.80[TSI][hapmap]
rs17187621	0.85[JPT][hapmap]
rs4979253	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518636	0.85[JPT][hapmap]
rs818714	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10739393	ALAD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116338200-116353600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:116340200-116355400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:116341600-116355800	Weak transcription	Fetal Brain Female	brain
4	chr9:116341800-116353600	Weak transcription	A549	lung
5	chr9:116342000-116355400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:116343200-116358800	Weak transcription	Hela-S3	cervix
7	chr9:116344800-116353800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:116344800-116355400	Weak transcription	Small Intestine	intestine
9	chr9:116346400-116355200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:116346600-116356800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:116346800-116353800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:116346800-116355800	Weak transcription	Brain Germinal Matrix	brain
13	chr9:116346800-116356000	Weak transcription	Ovary	ovary
14	chr9:116347000-116353400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:116347000-116353600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:116347200-116355800	Weak transcription	HSMMtube	muscle
17	chr9:116347400-116353600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:116348000-116353800	Weak transcription	Liver	Liver
19	chr9:116348000-116353800	Weak transcription	Fetal Lung	lung
20	chr9:116348000-116361600	Weak transcription	Dnd41	blood
21	chr9:116348200-116354000	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:116348200-116354200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:116348200-116356400	Weak transcription	Aorta	Aorta
24	chr9:116348400-116355600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:116348600-116353800	Weak transcription	HepG2	liver
26	chr9:116348600-116355600	Weak transcription	HMEC	breast
27	chr9:116348600-116355800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:116348800-116353800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:116349000-116353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:116349000-116355800	Enhancers	Adipose Nuclei	Adipose
31	chr9:116349000-116355800	Weak transcription	Fetal Intestine Large	intestine
32	chr9:116349200-116353800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:116349400-116353800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:116349600-116355600	Weak transcription	Osteobl	bone
35	chr9:116349800-116353800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr9:116349800-116354200	Weak transcription	Brain Angular Gyrus	brain
37	chr9:116350000-116353600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:116350000-116353600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:116350000-116353600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:116350000-116353800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:116350000-116353800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:116350000-116353800	Weak transcription	Esophagus	oesophagus
43	chr9:116350000-116355800	Weak transcription	HSMM	muscle
44	chr9:116350200-116353600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr9:116350200-116353600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:116350200-116353800	Weak transcription	Brain Anterior Caudate	brain
47	chr9:116350200-116355400	Weak transcription	NH-A	brain
48	chr9:116350400-116353600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:116350400-116353800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:116350400-116354200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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