Variant report

Variant	rs12098770
Chromosome Location	chr10:50288261-50288262
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	EP300	chr10:50288123-50288362	K562	blood:	n/a	n/a
2	CEBPB	chr10:50288046-50288313	K562	blood:	n/a	n/a
3	TBL1XR1	chr10:50288070-50288355	K562	blood:	n/a	n/a
4	MYC	chr10:50288080-50288388	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr10:50288074-50288544	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAFK	chr10:50287887-50288550	HepG2	liver:	n/a	chr10:50288507-50288518 chr10:50288508-50288519 chr10:50288507-50288518 chr10:50288506-50288520 chr10:50288508-50288519
7	MAX	chr10:50288143-50288410	NB4	blood:	n/a	n/a
8	FOS	chr10:50288034-50288385	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr10:50288073-50288554	HepG2	liver:	n/a	chr10:50288507-50288518 chr10:50288508-50288519 chr10:50288507-50288518 chr10:50288506-50288520 chr10:50288508-50288519
10	MYC	chr10:50288208-50288302	K562	blood:	n/a	n/a
11	UBTF	chr10:50288169-50288342	K562	blood:	n/a	n/a
12	STAT3	chr10:50287978-50288386	MCF10A-Er-Src	breast:	n/a	chr10:50288200-50288211
13	MAFF	chr10:50288113-50288313	HepG2	liver:	n/a	chr10:50288211-50288229
14	MAFK	chr10:50288056-50288408	K562	blood:	n/a	n/a
15	FOS	chr10:50288033-50288399	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr10:50288069-50288408	IMR90	lung:	n/a	n/a
17	STAT3	chr10:50288069-50288340	MCF10A-Er-Src	breast:	n/a	chr10:50288200-50288211
18	FOS	chr10:50288029-50288380	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr10:50288200-50288350	HCPEpiC	choroid plexus:	n/a	n/a
20	STAT3	chr10:50288032-50288362	MCF10A-Er-Src	breast:	n/a	chr10:50288200-50288211
21	STAT3	chr10:50288036-50288360	MCF10A-Er-Src	breast:	n/a	chr10:50288200-50288211
22	POLR2A	chr10:50288251-50288429	MCF10A-Er-Src	breast:	n/a	n/a
23	CTCF	chr10:50288240-50288390	HCPEpiC	choroid plexus:	n/a	n/a
24	STAT5A	chr10:50288029-50288402	K562	blood:	n/a	n/a
25	MAFK	chr10:50288178-50288369	H1-hESC	embryonic stem cell:	n/a	n/a
26	RCOR1	chr10:50288103-50288427	K562	blood:	n/a	n/a
27	MAX	chr10:50288150-50288506	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAFF	chr10:50288061-50288402	K562	blood:	n/a	chr10:50288211-50288229
29	STAT3	chr10:50288039-50288385	MCF10A-Er-Src	breast:	n/a	chr10:50288200-50288211
30	MYC	chr10:50288102-50288404	NB4	blood:	n/a	n/a
31	FOS	chr10:50288053-50288383	MCF10A-Er-Src	breast:	n/a	n/a
32	HCFC1	chr10:50288212-50288283	K562	blood:	n/a	n/a
33	JUND	chr10:50288102-50288391	K562	blood:	n/a	n/a
34	TEAD4	chr10:50287995-50288389	K562	blood:	n/a	n/a
35	MAX	chr10:50288229-50288544	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F6	chr10:50288177-50288528	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F6	chr10:50288136-50288570	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50287416..50289075-chr10:50291865..50294530,2	MCF-7	breast:
2	chr10:50288196..50290467-chr10:50297375..50300354,2	K562	blood:

Variant related genes	Relation type
VSTM4	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10508911	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10857434	0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11100985	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs17699932	1.00[CHD][hapmap]
rs4129034	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393232	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437954	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	esv2761593	chr10:50276812-50336129	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50266600-50289400	Weak transcription	Colonic Mucosa	Colon
2	chr10:50267200-50288400	Weak transcription	NHLF	lung
3	chr10:50272600-50294200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr10:50273600-50289800	Weak transcription	NHDF-Ad	bronchial
5	chr10:50279600-50289200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:50279800-50288600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:50280600-50288600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:50281600-50288400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:50282400-50289400	Weak transcription	Fetal Kidney	kidney
10	chr10:50283200-50288600	Weak transcription	Placenta	Placenta
11	chr10:50283200-50298200	Weak transcription	Spleen	Spleen
12	chr10:50284000-50288600	Weak transcription	Esophagus	oesophagus
13	chr10:50284600-50288400	Weak transcription	Aorta	Aorta
14	chr10:50284600-50288600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:50284800-50292400	Enhancers	Liver	Liver
16	chr10:50285200-50292400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr10:50285400-50288400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr10:50285400-50288400	Weak transcription	Pancreas	Pancrea
19	chr10:50285400-50289200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:50285400-50289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:50285600-50288400	Weak transcription	Brain Anterior Caudate	brain
22	chr10:50285600-50288400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:50285600-50288400	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:50285600-50288600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:50286000-50292400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:50286800-50289600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:50287000-50290200	Enhancers	Fetal Intestine Small	intestine
28	chr10:50287200-50289400	Enhancers	Primary hematopoietic stem cells	blood
29	chr10:50287200-50290000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr10:50287200-50290400	Enhancers	K562	blood
31	chr10:50287200-50292200	Enhancers	Adipose Nuclei	Adipose
32	chr10:50287200-50292400	Enhancers	Brain Substantia Nigra	brain
33	chr10:50287400-50288400	Weak transcription	Ovary	ovary
34	chr10:50287400-50288400	Weak transcription	HSMMtube	muscle
35	chr10:50287400-50289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr10:50287400-50289000	Weak transcription	Lung	lung
37	chr10:50287600-50289000	Enhancers	HSMM	muscle
38	chr10:50287600-50290400	Enhancers	Fetal Intestine Large	intestine
39	chr10:50288000-50291400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr10:50288000-50291400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr10:50288200-50288400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:50288200-50288400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr10:50288200-50288400	Enhancers	Fetal Thymus	thymus
44	chr10:50288200-50288400	Enhancers	Gastric	stomach
45	chr10:50288200-50288600	Active TSS	Fetal Brain Male	brain
46	chr10:50288200-50288800	Enhancers	Fetal Lung	lung
47	chr10:50288200-50289200	Enhancers	Stomach Smooth Muscle	stomach
48	chr10:50288200-50289800	Enhancers	Right Atrium	heart
49	chr10:50288200-50291000	Enhancers	Fetal Muscle Leg	muscle
50	chr10:50288200-50291400	Enhancers	Brain Angular Gyrus	brain

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