Variant report

Variant	rs10508590
Chromosome Location	chr10:19927472-19927473
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	chr10:19927138-19927873	Hela-S3	cervix:	n/a	chr10:19927779-19927793 chr10:19927489-19927503 chr10:19927783-19927792 chr10:19927490-19927499
2	TCF7L2	chr10:19927138-19927766	Hela-S3	cervix:	n/a	n/a
3	NR2F2	chr10:19927357-19927843	MCF-7	breast:	n/a	n/a
4	FOSL2	chr10:19927132-19927899	SK-N-SH	brain:	n/a	chr10:19927781-19927790
5	RXRA	chr10:19927242-19927997	SK-N-SH	brain:	n/a	chr10:19927676-19927689 chr10:19927494-19927503 chr10:19927677-19927688
6	NFIC	chr10:19927398-19927831	SK-N-SH	brain:	n/a	chr10:19927716-19927733
7	TCF12	chr10:19927059-19928038	SK-N-SH	brain:	n/a	chr10:19927977-19927984 chr10:19927279-19927288 chr10:19927768-19927777
8	RAD21	chr10:19927180-19927821	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr10:19927445-19927854	Hela-S3	cervix:	n/a	n/a
10	MAFK	chr10:19927466-19927888	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr10:19927441-19927876	IMR90	lung:	n/a	chr10:19927714-19927725
12	PBX3	chr10:19927301-19927987	SK-N-SH	brain:	n/a	n/a
13	MEF2A	chr10:19927258-19927982	SK-N-SH	brain:	n/a	chr10:19927366-19927381 chr10:19927366-19927381
14	MAFK	chr10:19927461-19927813	HepG2	liver:	n/a	n/a
15	FOS	chr10:19927215-19927773	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr10:19927292-19927931	IMR90	lung:	n/a	n/a
17	POLR2A	chr10:19927429-19927852	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr10:19927121-19928007	SK-N-SH	brain:	n/a	chr10:19927977-19927984 chr10:19927279-19927288 chr10:19927768-19927777
19	CEBPB	chr10:19927189-19927896	Hela-S3	cervix:	n/a	chr10:19927714-19927725
20	NFIC	chr10:19927223-19928027	SK-N-SH	brain:	n/a	chr10:19927716-19927733
21	PBX3	chr10:19927141-19927927	SK-N-SH	brain:	n/a	n/a
22	EP300	chr10:19927453-19927786	SK-N-SH_RA	brain:	n/a	chr10:19927489-19927503 chr10:19927490-19927499
23	RFX5	chr10:19927355-19927854	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr10:19927126-19927887	SK-N-SH	brain:	n/a	chr10:19927491-19927501
25	FOXA1	chr10:19927397-19927899	HepG2	liver:	n/a	n/a
26	NR2F2	chr10:19927350-19927971	MCF-7	breast:	n/a	n/a
27	TEAD4	chr10:19927347-19928008	SK-N-SH	brain:	n/a	chr10:19927584-19927593 chr10:19927498-19927507
28	CEBPB	chr10:19927464-19927923	MCF-7	breast:	n/a	chr10:19927714-19927725
29	JUND	chr10:19927304-19927827	HepG2	liver:	n/a	chr10:19927781-19927790
30	GATA3	chr10:19927424-19927930	MCF-7	breast:	n/a	chr10:19927491-19927501
31	TEAD4	chr10:19927381-19927829	HepG2	liver:	n/a	chr10:19927584-19927593 chr10:19927498-19927507
32	EP300	chr10:19927301-19928087	SK-N-SH	brain:	n/a	chr10:19927779-19927793 chr10:19927489-19927503 chr10:19927783-19927792 chr10:19927976-19927990 chr10:19927490-19927499
33	MYC	chr10:19927388-19927896	MCF10A-Er-Src	breast:	n/a	n/a
34	EP300	chr10:19927187-19928072	SK-N-SH	brain:	n/a	chr10:19927779-19927793 chr10:19927489-19927503 chr10:19927783-19927792 chr10:19927976-19927990 chr10:19927490-19927499
35	GATA3	chr10:19927226-19928059	SK-N-SH	brain:	n/a	chr10:19927491-19927501
36	JUND	chr10:19927258-19927884	SK-N-SH	brain:	n/a	chr10:19927781-19927790
37	TEAD4	chr10:19927232-19927998	SK-N-SH	brain:	n/a	chr10:19927584-19927593 chr10:19927498-19927507
38	MAFK	chr10:19927459-19927826	HepG2	liver:	n/a	n/a
39	HNF4A	chr10:19927471-19927821	HepG2	liver:	n/a	chr10:19927651-19927664 chr10:19927651-19927665 chr10:19927649-19927667 chr10:19927652-19927664 chr10:19927770-19927778 chr10:19927650-19927665 chr10:19927652-19927664
40	FOXA2	chr10:19927454-19927779	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNA5SP303	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10508588	0.88[EUR][1000 genomes]
rs10508589	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10827679	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10827696	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10827723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827728	0.85[EUR][1000 genomes]
rs10827732	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827733	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827734	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827735	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827736	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827738	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10827743	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11010652	0.89[EUR][1000 genomes]
rs11010662	0.85[EUR][1000 genomes]
rs11010792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11010794	0.88[EUR][1000 genomes]
rs11010795	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11010796	0.88[EUR][1000 genomes]
rs11010817	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11010877	1.00[EUR][1000 genomes]
rs11010881	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11010886	0.88[EUR][1000 genomes]
rs11010896	0.83[EUR][1000 genomes]
rs11010900	0.81[AFR][1000 genomes]
rs11010903	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11010972	0.83[EUR][1000 genomes]
rs11011078	0.81[EUR][1000 genomes]
rs12249987	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12258971	0.81[AFR][1000 genomes]
rs12259525	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12259745	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12261044	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12261359	0.88[EUR][1000 genomes]
rs12262868	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12263598	0.83[EUR][1000 genomes]
rs12268966	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12358323	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12776678	1.00[CEU][hapmap]
rs12777618	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1326966	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1326972	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1326986	1.00[EUR][1000 genomes]
rs1326988	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1326990	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1326991	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1854075	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2225082	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35749706	0.86[EUR][1000 genomes]
rs7474617	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466764	chr10:19400845-19979434	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv550128	chr10:19400845-19979434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2759737	chr10:19694144-20024994	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2758211	chr10:19714637-20024994	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1042877	chr10:19749314-20067572	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2757373	chr10:19776910-20004996	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv34306	chr10:19777069-20117944	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv3518965	chr10:19786251-20061305	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3518966	chr10:19786310-20061256	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv894931	chr10:19796958-19987644	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv825266	chr10:19807019-20037182	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv831804	chr10:19859400-20035593	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv894933	chr10:19865757-20036080	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:19926000-19927800	Enhancers	HSMMtube	muscle
2	chr10:19926200-19927600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:19926400-19927600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:19926400-19927600	Enhancers	HSMM	muscle
5	chr10:19926400-19927800	Enhancers	HMEC	breast
6	chr10:19926600-19927600	Enhancers	Fetal Intestine Large	intestine
7	chr10:19926600-19927600	Enhancers	Fetal Intestine Small	intestine
8	chr10:19926600-19927600	Enhancers	Hela-S3	cervix
9	chr10:19926600-19927800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:19926600-19927800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:19926800-19927600	Weak transcription	Placenta	Placenta
12	chr10:19926800-19927600	Weak transcription	Psoas Muscle	Psoas
13	chr10:19926800-19928200	Active TSS	NHLF	lung
14	chr10:19927000-19927600	Enhancers	Fetal Kidney	kidney
15	chr10:19927000-19927800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:19927000-19928000	Active TSS	NHDF-Ad	bronchial
17	chr10:19927000-19928200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr10:19927200-19927600	Enhancers	Brain Hippocampus Middle	brain
19	chr10:19927200-19927600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr10:19927200-19927600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr10:19927200-19927800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:19927200-19928000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:19927200-19928000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:19927200-19928000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr10:19927200-19928000	Active TSS	Ovary	ovary
26	chr10:19927200-19928000	Active TSS	Right Atrium	heart
27	chr10:19927200-19928000	Active TSS	A549	lung
28	chr10:19927200-19928200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:19927200-19928200	Active TSS	Fetal Lung	lung
30	chr10:19927400-19927600	Enhancers	Primary hematopoietic stem cells	blood
31	chr10:19927400-19927600	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr10:19927400-19927600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr10:19927400-19927600	Flanking Active TSS	NH-A	brain
34	chr10:19927400-19927800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:19927400-19927800	Flanking Active TSS	Liver	Liver
36	chr10:19927400-19927800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr10:19927400-19927800	Active TSS	Rectal Smooth Muscle	rectum
38	chr10:19927400-19927800	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr10:19927400-19927800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr10:19927400-19927800	Flanking Active TSS	HepG2	liver
41	chr10:19927400-19927800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr10:19927400-19928000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:19927400-19928000	Active TSS	Aorta	Aorta
44	chr10:19927400-19928000	Active TSS	Colon Smooth Muscle	Colon
45	chr10:19927400-19928000	Active TSS	Fetal Stomach	stomach
46	chr10:19927400-19928000	Active TSS	Osteobl	bone
47	chr10:19927400-19928200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:19927400-19928200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr10:19927400-19928200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr10:19927400-19928200	Active TSS	Rectal Mucosa Donor 29	rectum

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