Variant report

Variant	rs10497500
Chromosome Location	chr2:178467748-178467749
allele	C/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	HNF4G	chr2:178467429-178467979	HepG2	liver:	n/a	chr2:178467800-178467812 chr2:178467800-178467812 chr2:178467800-178467813 chr2:178467800-178467812 chr2:178467800-178467812
2	HDAC2	chr2:178467575-178467969	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:178467499-178468071	HepG2	liver:	n/a	n/a
4	MAX	chr2:178466872-178468052	HepG2	liver:	n/a	n/a
5	TBP	chr2:178467578-178467859	HepG2	liver:	n/a	n/a
6	SP1	chr2:178467485-178467979	HepG2	liver:	n/a	n/a
7	HNF4A	chr2:178467602-178467972	HepG2	liver:	n/a	chr2:178467800-178467812 chr2:178467798-178467813 chr2:178467800-178467812 chr2:178467800-178467813 chr2:178467800-178467812 chr2:178467800-178467812
8	FOXA2	chr2:178467584-178467962	HepG2	liver:	n/a	n/a
9	HEY1	chr2:178467619-178467985	HepG2	liver:	n/a	n/a
10	FOXA2	chr2:178467277-178468273	HepG2	liver:	n/a	n/a
11	MBD4	chr2:178466797-178468029	HepG2	liver:	n/a	n/a
12	TEAD4	chr2:178467316-178468011	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:178467236-178468055	HepG2	liver:	n/a	n/a
14	NFIC	chr2:178466811-178468082	HepG2	liver:	n/a	n/a
15	MYBL2	chr2:178467363-178468119	HepG2	liver:	n/a	n/a
16	FOXA1	chr2:178467461-178468069	HepG2	liver:	n/a	n/a
17	ARID3A	chr2:178467332-178467994	HepG2	liver:	n/a	n/a
18	RCOR1	chr2:178467650-178467945	HepG2	liver:	n/a	n/a
19	CEBPB	chr2:178467653-178467850	HepG2	liver:	n/a	n/a
20	MYBL2	chr2:178467456-178468065	HepG2	liver:	n/a	n/a
21	RAD21	chr2:178467676-178468015	HepG2	liver:	n/a	n/a
22	SMC3	chr2:178467466-178467883	HepG2	liver:	n/a	n/a
23	FOXA1	chr2:178467495-178468084	HepG2	liver:	n/a	n/a
24	HNF4G	chr2:178467449-178468021	HepG2	liver:	n/a	chr2:178467800-178467812 chr2:178467800-178467812 chr2:178467800-178467813 chr2:178467800-178467812 chr2:178467800-178467812
25	HNF4A	chr2:178467579-178467958	HepG2	liver:	n/a	chr2:178467800-178467812 chr2:178467798-178467813 chr2:178467800-178467812 chr2:178467800-178467813 chr2:178467800-178467812 chr2:178467800-178467812
26	EP300	chr2:178467547-178467935	HepG2	liver:	n/a	n/a
27	EP300	chr2:178467538-178467909	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000237655	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10196345	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10201153	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs10497501	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12612857	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12615367	0.85[JPT][hapmap]
rs12616093	0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs13004955	0.85[JPT][hapmap]
rs13403787	0.83[ASN][1000 genomes]
rs13404970	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13417231	0.85[ASN][1000 genomes]
rs13430517	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13432183	0.83[ASN][1000 genomes]
rs1348850	0.85[JPT][hapmap]
rs1405713	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1545364	0.83[ASN][1000 genomes]
rs1548067	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs16865328	0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs16865331	0.86[JPT][hapmap]
rs16865433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213945	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs4243390	0.83[ASN][1000 genomes]
rs4528793	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4893959	0.86[JPT][hapmap]
rs4893961	0.86[JPT][hapmap]
rs4893962	0.86[JPT][hapmap]
rs4893965	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs57562172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59666005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60642012	0.82[EUR][1000 genomes]
rs6710575	0.85[JPT][hapmap]
rs6717572	0.82[EUR][1000 genomes]
rs7604673	0.85[JPT][hapmap]
rs7606235	0.86[JPT][hapmap]
rs8941	0.86[JPT][hapmap]
rs9288004	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9288005	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178458600-178467800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:178462000-178468600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:178462800-178469000	Weak transcription	Small Intestine	intestine
4	chr2:178462800-178475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:178463200-178471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:178463200-178471200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:178463600-178468600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:178463800-178475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:178464200-178468600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:178464200-178469200	Weak transcription	Brain Anterior Caudate	brain
12	chr2:178464200-178471200	Weak transcription	HUVEC	blood vessel
13	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
14	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:178464400-178467800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:178464400-178469000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:178464400-178469000	Weak transcription	Left Ventricle	heart
18	chr2:178464600-178468200	Weak transcription	Adipose Nuclei	Adipose
19	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:178465600-178469400	Enhancers	Fetal Muscle Leg	muscle
21	chr2:178466000-178468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:178466800-178468400	Enhancers	Fetal Stomach	stomach
23	chr2:178467000-178468000	Flanking Active TSS	HepG2	liver
24	chr2:178467000-178468600	Enhancers	Fetal Intestine Small	intestine
25	chr2:178467000-178469200	Enhancers	Fetal Intestine Large	intestine
26	chr2:178467200-178467800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:178467400-178467800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:178467400-178468000	Enhancers	Duodenum Mucosa	Duodenum
29	chr2:178467400-178468200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:178467400-178468200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:178467400-178469000	Enhancers	Fetal Brain Female	brain
32	chr2:178467600-178468000	Flanking Active TSS	Fetal Kidney	kidney
33	chr2:178467600-178468000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr2:178467600-178468400	Enhancers	Fetal Brain Male	brain
35	chr2:178467600-178468400	Flanking Active TSS	Fetal Lung	lung
36	chr2:178467600-178469000	Enhancers	Ovary	ovary
37	chr2:178467600-178469200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr2:178467600-178469400	Enhancers	Liver	Liver

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