Variant report

Variant	rs1062176
Chromosome Location	chr10:98346649-98346650
allele	A/C
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	POLR2A	chr10:98345763-98347305	HL-60	blood:	n/a	n/a
2	POLR2A	chr10:98345926-98347572	PFSK-1	brain:	n/a	n/a
3	CHD1	chr10:98346213-98347406	GM12878	blood:	n/a	chr10:98346594-98346604
4	MYC	chr10:98345601-98347312	NB4	blood:	n/a	n/a
5	POLR2A	chr10:98346029-98347197	A549	lung:	n/a	n/a
6	POLR2A	chr10:98346172-98347281	ProgFib	skin:	n/a	n/a
7	POLR2A	chr10:98345931-98347317	Hela-S3	cervix:	n/a	n/a
8	RELA	chr10:98346339-98347836	GM10847	blood:	n/a	n/a
9	POLR2A	chr10:98346649-98347181	GM12891	blood:	n/a	n/a
10	TCF7L2	chr10:98346306-98347145	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr10:98346122-98347180	GM10847	blood:	n/a	n/a
12	TBP	chr10:98346178-98347535	HepG2	liver:	n/a	n/a
13	IRF1	chr10:98346254-98347838	K562	blood:	n/a	chr10:98346773-98346787
14	POLR2A	chr10:98346522-98347442	U87	brain:	n/a	n/a
15	GABPA	chr10:98346088-98347161	HepG2	liver:	n/a	chr10:98346910-98346919 chr10:98346976-98346985 chr10:98346777-98346786
16	TAF1	chr10:98346065-98347137	HepG2	liver:	n/a	n/a
17	TAF7	chr10:98346591-98347183	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr10:98346088-98347130	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr10:98346613-98347241	GM12892	blood:	n/a	n/a
20	MAX	chr10:98346223-98347313	HepG2	liver:	n/a	n/a
21	POLR2A	chr10:98346514-98347255	H1-hESC	embryonic stem cell:	n/a	n/a
22	POU2F2	chr10:98346575-98347293	GM12878	blood:	n/a	chr10:98346783-98346795 chr10:98346777-98346789
23	MYC	chr10:98345782-98347262	K562	blood:	n/a	n/a
24	POLR2A	chr10:98346584-98347147	HepG2	liver:	n/a	n/a
25	POLR2A	chr10:98346193-98347103	A549	lung:	n/a	n/a
26	HEY1	chr10:98346148-98347138	K562	blood:	n/a	chr10:98346834-98346849 chr10:98346912-98346927 chr10:98346598-98346613 chr10:98346973-98346988
27	SIN3AK20	chr10:98346087-98346667	H1-hESC	embryonic stem cell:	n/a	n/a
28	EP300	chr10:98346236-98347340	K562	blood:	n/a	chr10:98346846-98346853 chr10:98346976-98346985 chr10:98346779-98346795
29	REST	chr10:98346555-98347287	PFSK-1	brain:	n/a	n/a
30	PML	chr10:98346541-98347105	MCF-7	breast:	n/a	n/a
31	CREB1	chr10:98346084-98347110	HepG2	liver:	n/a	chr10:98346815-98346828
32	CTCF	chr10:98346133-98346722	K562	blood:	n/a	n/a
33	GABPA	chr10:98346092-98347031	H1-hESC	embryonic stem cell:	n/a	chr10:98346910-98346919 chr10:98346976-98346985 chr10:98346777-98346786
34	CHD2	chr10:98346493-98346954	K562	blood:	n/a	chr10:98346594-98346604
35	FOXP2	chr10:98346118-98347102	PFSK-1	brain:	n/a	n/a
36	EP300	chr10:98346565-98347009	T-47D	breast:	n/a	chr10:98346846-98346853 chr10:98346976-98346985 chr10:98346779-98346795
37	USF1	chr10:98346623-98346993	SK-N-SH	brain:	n/a	n/a
38	JUND	chr10:98346098-98347169	A549	lung:	n/a	chr10:98346778-98346787 chr10:98346807-98346818
39	BHLHE40	chr10:98346199-98347251	HepG2	liver:	n/a	n/a
40	YY1	chr10:98345953-98347294	ECC-1	luminal epithelium:	n/a	chr10:98346919-98346930 chr10:98346869-98346883 chr10:98346156-98346167 chr10:98346774-98346785 chr10:98346777-98346786 chr10:98346872-98346886
41	POLR2A	chr10:98345510-98347401	GM12891	blood:	n/a	n/a
42	POLR2A	chr10:98345782-98347348	GM12892	blood:	n/a	n/a
43	POLR2A	chr10:98346046-98347207	HepG2	liver:	n/a	n/a
44	POLR2A	chr10:98346024-98347314	GM18526	blood:	n/a	n/a
45	SIN3A	chr10:98346203-98347081	GM12878	blood:	n/a	n/a
46	RUNX3	chr10:98346579-98347217	GM12878	blood:	n/a	n/a
47	CREB1	chr10:98346639-98347102	GM12878	blood:	n/a	chr10:98346815-98346828
48	HEY1	chr10:98346058-98347205	K562	blood:	n/a	chr10:98346834-98346849 chr10:98346912-98346927 chr10:98346598-98346613 chr10:98346973-98346988
49	FOXA1	chr10:98346631-98346983	T-47D	breast:	n/a	n/a
50	MAZ	chr10:98346239-98347411	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:98346445..98347105-chr3:52719196..52720083,2	Hela-S3	cervix:
2	chr10:98346273..98347080-chr13:111367287..111368137,2	Hela-S3	cervix:
3	chr10:98336275..98339517-chr10:98344498..98348223,6	MCF-7	breast:
4	chr10:98346272..98347070-chr19:10613208..10614006,2	NB4	blood:
5	chr10:98346001..98346671-chr11:10830156..10831102,2	Hela-S3	cervix:
6	chr10:98346358..98347264-chr12:31478554..31479072,2	Hela-S3	cervix:
7	chr10:98346336..98346846-chr19:33667684..33668254,2	Hela-S3	cervix:
8	chr1:43855378..43855887-chr10:98346254..98347186,2	Hela-S3	cervix:
9	chr10:98345733..98347828-chr10:98591279..98593531,2	MCF-7	breast:
10	chr1:25573131..25573708-chr10:98346304..98347301,2	Hela-S3	cervix:
11	chr10:98346265..98346836-chr17:45972611..45973150,2	Hela-S3	cervix:
12	chr10:98344586..98349024-chr10:98390080..98394763,4	MCF-7	breast:
13	chr10:98345353..98347090-chr10:98380383..98383295,2	K562	blood:
14	chr10:98346447..98347210-chr5:87564239..87564953,2	NB4	blood:
15	chr10:98345052..98347789-chr10:98590945..98593407,3	K562	blood:
16	chr1:28908124..28908849-chr10:98346320..98346849,2	Hela-S3	cervix:
17	chr1:109203195..109203852-chr10:98346013..98346805,2	Hela-S3	cervix:

Variant related genes	Relation type
TM9SF3	TF binding region
ENSG00000227032	Chromatin interaction
ENSG00000196233	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000197989	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000155629	Chromatin interaction
ENSG00000077147	Chromatin interaction
ENSG00000117616	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000159479	Chromatin interaction
ENSG00000198198	Chromatin interaction
ENSG00000164180	Chromatin interaction
ENSG00000247828	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000162639	Chromatin interaction
ENSG00000264355	Chromatin interaction
ENSG00000079999	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1063605	0.82[EUR][1000 genomes]
rs11188831	0.81[EUR][1000 genomes]
rs11188840	0.84[EUR][1000 genomes]
rs11188842	0.84[EUR][1000 genomes]
rs11188844	0.83[EUR][1000 genomes]
rs3748237	0.81[EUR][1000 genomes]
rs61859300	0.84[EUR][1000 genomes]
rs7070686	0.84[EUR][1000 genomes]
rs7071044	0.84[EUR][1000 genomes]
rs7074516	0.82[EUR][1000 genomes]
rs7086213	0.82[EUR][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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3358283	chr10:98345587-98348135	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
3	esv3446584	chr10:98345712-98347935	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98344400-98347200	Active TSS	HSMM	muscle
2	chr10:98344400-98347200	Active TSS	NHLF	lung
3	chr10:98344400-98347400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:98344400-98347600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr10:98344400-98347600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr10:98344600-98347200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:98344600-98347400	Active TSS	Fetal Intestine Large	intestine
8	chr10:98344600-98347400	Active TSS	Fetal Intestine Small	intestine
9	chr10:98344600-98347600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:98344600-98347600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:98344600-98347800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr10:98344600-98347800	Active TSS	Right Ventricle	heart
13	chr10:98344800-98347200	Active TSS	Fetal Thymus	thymus
14	chr10:98344800-98347200	Active TSS	HMEC	breast
15	chr10:98344800-98347200	Active TSS	HSMMtube	muscle
16	chr10:98344800-98347400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr10:98344800-98347600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:98344800-98347600	Active TSS	NHDF-Ad	bronchial
19	chr10:98344800-98348000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:98345000-98347200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr10:98345000-98347400	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr10:98345000-98347400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr10:98345000-98347400	Active TSS	GM12878-XiMat	blood
24	chr10:98345000-98347600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr10:98345000-98347600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:98345000-98347600	Active TSS	A549	lung
27	chr10:98345000-98347800	Active TSS	Right Atrium	heart
28	chr10:98345000-98347800	Active TSS	Thymus	Thymus
29	chr10:98345200-98347000	Active TSS	Placenta	Placenta
30	chr10:98345200-98347200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:98345200-98347400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr10:98345200-98347600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr10:98345200-98347600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:98345200-98347800	Active TSS	Ovary	ovary
35	chr10:98345200-98348000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:98345200-98348000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr10:98345400-98347200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:98345400-98347200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr10:98345400-98347400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:98345400-98347400	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr10:98345400-98347400	Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr10:98345400-98347400	Active TSS	NHEK	skin
43	chr10:98345400-98347600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:98345400-98347600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:98345400-98347600	Active TSS	Left Ventricle	heart
46	chr10:98345400-98347600	Active TSS	Small Intestine	intestine
47	chr10:98345400-98347600	Active TSS	Stomach Mucosa	stomach
48	chr10:98345400-98347800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr10:98345400-98347800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr10:98345400-98348000	Active TSS	Aorta	Aorta

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