Variant report

Variant	rs12956170
Chromosome Location	chr18:8827166-8827167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:8826875-8827236	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr18:8827016-8827347	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr18:8826925-8827376	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr18:8827078-8827252	A549	lung:	n/a	n/a
5	POLR2A	chr18:8826706-8827470	K562	blood:	n/a	n/a
6	POLR2A	chr18:8827020-8827334	A549	lung:	n/a	n/a
7	POLR2A	chr18:8827092-8827288	A549	lung:	n/a	n/a
8	POLR2A	chr18:8827095-8827438	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr18:8826080-8827560	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:8814066..8816178-chr18:8827038..8829489,2	MCF-7	breast:
2	chr18:8827151..8829025-chr18:8829102..8831478,2	K562	blood:
3	chr18:8808921..8812176-chr18:8824386..8827624,3	K562	blood:

No data

Variant related genes	Relation type
SOGA2	TF binding region
ENSG00000168502	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10432143	0.83[ASN][1000 genomes]
rs11081410	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs12956773	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs12957034	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs1564484	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2170297	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2242273	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs34740257	0.95[ASN][1000 genomes]
rs35950206	0.81[ASN][1000 genomes]
rs595802	0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs71362044	0.81[ASN][1000 genomes]
rs7233770	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7240816	1.00[CHB][hapmap];0.90[ASN][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	nsv1064883	chr18:8709670-9133224	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
2	nsv833584	chr18:8728616-8904213	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv909363	chr18:8775184-8858086	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8789400-8829800	Weak transcription	Brain Anterior Caudate	brain
2	chr18:8801200-8828200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr18:8801200-8834800	Weak transcription	Esophagus	oesophagus
4	chr18:8802400-8830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:8805400-8829200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr18:8805600-8827600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr18:8806200-8828600	Weak transcription	Lung	lung
8	chr18:8807000-8827600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr18:8807800-8835200	Weak transcription	Right Ventricle	heart
10	chr18:8811400-8828800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr18:8813800-8828600	Weak transcription	Adipose Nuclei	Adipose
12	chr18:8817000-8827600	Strong transcription	NH-A	brain
13	chr18:8817000-8828000	Strong transcription	NHLF	lung
14	chr18:8817000-8830400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:8817200-8828200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr18:8817200-8828600	Strong transcription	NHDF-Ad	bronchial
17	chr18:8817200-8834800	Weak transcription	Psoas Muscle	Psoas
18	chr18:8817400-8828000	Strong transcription	HSMM	muscle
19	chr18:8817600-8827600	Strong transcription	Osteobl	bone
20	chr18:8817800-8827400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr18:8817800-8830800	Strong transcription	Fetal Stomach	stomach
22	chr18:8819000-8827200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr18:8819800-8828800	Weak transcription	Brain Substantia Nigra	brain
24	chr18:8821200-8827600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr18:8821400-8830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr18:8821400-8831600	Weak transcription	Aorta	Aorta
27	chr18:8821400-8834600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr18:8821600-8828200	Weak transcription	Hela-S3	cervix
29	chr18:8821600-8834800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:8821800-8828600	Strong transcription	A549	lung
31	chr18:8822000-8829400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr18:8822200-8827600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr18:8822400-8836800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:8822800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:8822800-8827800	Strong transcription	Brain Germinal Matrix	brain
36	chr18:8823200-8831800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr18:8824000-8827200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr18:8824200-8828200	Weak transcription	Fetal Heart	heart
39	chr18:8824400-8827200	Weak transcription	Left Ventricle	heart
40	chr18:8824400-8828800	Weak transcription	Spleen	Spleen
41	chr18:8824600-8827400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:8824600-8827600	Strong transcription	HSMMtube	muscle
43	chr18:8824800-8827200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr18:8824800-8827400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:8825000-8827200	Strong transcription	HUVEC	blood vessel
46	chr18:8825000-8827400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr18:8825000-8828600	Weak transcription	Right Atrium	heart
48	chr18:8825400-8828000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr18:8825400-8828800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr18:8825400-8829800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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