Variant report

Variant	rs9462062
Chromosome Location	chr6:35181455-35181456
allele	G/T
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	MXI1	chr6:35181249-35181842	H1-hESC	embryonic stem cell:	n/a	chr6:35181437-35181452 chr6:35181439-35181454
2	POLR2A	chr6:35181028-35182507	H1-neurons	neurons:	n/a	n/a
3	TEAD4	chr6:35181267-35181681	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZBTB7A	chr6:35181366-35182192	ECC-1	luminal epithelium:	n/a	n/a
5	ZNF143	chr6:35181379-35181953	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr6:35181389-35181513	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr6:35181269-35181920	H1-hESC	embryonic stem cell:	n/a	chr6:35181885-35181894 chr6:35181888-35181899 chr6:35181889-35181903 chr6:35181885-35181896 chr6:35181888-35181897
8	TEAD4	chr6:35181238-35181717	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr6:35181193-35182456	H1-hESC	embryonic stem cell:	n/a	chr6:35181443-35181452 chr6:35181919-35181929 chr6:35181439-35181448
10	CTBP2	chr6:35181103-35182305	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr6:35181215-35182090	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr6:35181187-35181491	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF1	chr6:35181047-35182112	H1-neurons	neurons:	n/a	n/a
14	ZNF263	chr6:35181349-35181987	HEK293-T-REx	kidney:	n/a	chr6:35181670-35181691 chr6:35181691-35181712
15	REST	chr6:35180725-35183005	H1-neurons	neurons:	n/a	chr6:35182310-35182323 chr6:35182307-35182327 chr6:35181895-35181908 chr6:35182415-35182428 chr6:35180964-35180974 chr6:35181102-35181115 chr6:35182307-35182327 chr6:35182371-35182384 chr6:35181504-35181517
16	POLR2A	chr6:35181072-35182512	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr6:35181241-35181468	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr6:35181177-35182038	H1-neurons	neurons:	n/a	n/a
19	SIN3A	chr6:35180939-35182758	H1-hESC	embryonic stem cell:	n/a	chr6:35180965-35180974 chr6:35182362-35182371 chr6:35182415-35182428 chr6:35182169-35182180 chr6:35182477-35182488 chr6:35182307-35182320
20	CHD2	chr6:35181388-35181526	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:35177824..35181731-chr6:35185438..35190079,5	K562	blood:

Variant related genes	Relation type
SCUBE3	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1034450	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10428744	1.00[ASN][1000 genomes]
rs11962521	1.00[ASN][1000 genomes]
rs11962524	1.00[ASN][1000 genomes]
rs12110520	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110664	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111424	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16868695	1.00[ASN][1000 genomes]
rs16868699	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16872293	1.00[ASN][1000 genomes]
rs16874062	0.81[AMR][1000 genomes]
rs16874216	1.00[ASN][1000 genomes]
rs16874262	0.81[AMR][1000 genomes]
rs2004	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187903	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228265	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627111	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2894400	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34278260	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35455943	0.88[EUR][1000 genomes]
rs41270046	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270062	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45482297	1.00[ASN][1000 genomes]
rs56809926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57229653	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57468283	1.00[ASN][1000 genomes]
rs57794912	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57976333	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58796597	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58850273	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59895076	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60086237	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60113507	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60569490	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61592141	1.00[ASN][1000 genomes]
rs61734578	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457817	1.00[ASN][1000 genomes]
rs6900879	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901580	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904477	1.00[ASN][1000 genomes]
rs6905732	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906117	0.81[AMR][1000 genomes]
rs6911817	1.00[ASN][1000 genomes]
rs6923025	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934083	1.00[ASN][1000 genomes]
rs6938138	1.00[ASN][1000 genomes]
rs6939017	1.00[ASN][1000 genomes]
rs73403830	1.00[ASN][1000 genomes]
rs73403834	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403837	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403843	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403847	1.00[ASN][1000 genomes]
rs73403887	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405709	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405725	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405759	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405765	1.00[ASN][1000 genomes]
rs73405768	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405774	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405795	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405799	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407610	1.00[ASN][1000 genomes]
rs73407613	1.00[ASN][1000 genomes]
rs73407619	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407641	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407675	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409710	1.00[ASN][1000 genomes]
rs73409758	1.00[ASN][1000 genomes]
rs73409765	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409769	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409774	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409778	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409793	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411706	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411720	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411726	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73411781	0.81[EUR][1000 genomes]
rs73411797	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746425	1.00[ASN][1000 genomes]
rs743965	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773319	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820102	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462064	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462066	0.81[AMR][1000 genomes]
rs9469960	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469965	0.81[AMR][1000 genomes]
rs9469966	0.81[AMR][1000 genomes]
rs9469967	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469969	0.87[AMR][1000 genomes]
rs9469977	0.81[AMR][1000 genomes]
rs9469984	0.81[AMR][1000 genomes]
rs9658127	1.00[ASN][1000 genomes]
rs9658131	1.00[ASN][1000 genomes]
rs9942465	0.81[EUR][1000 genomes];1.00[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	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35180400-35182600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:35180800-35181600	Flanking Active TSS	Fetal Heart	heart
3	chr6:35180800-35182200	Bivalent/Poised TSS	Fetal Brain Female	brain
4	chr6:35181000-35181600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr6:35181000-35181600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:35181000-35181600	Bivalent Enhancer	Placenta	Placenta
7	chr6:35181000-35181600	Enhancers	Lung	lung
8	chr6:35181000-35181800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:35181000-35181800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
10	chr6:35181000-35182000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
11	chr6:35181000-35182200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
12	chr6:35181000-35182400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
13	chr6:35181000-35182600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:35181000-35182600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:35181000-35182600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:35181000-35182600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:35181000-35182600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:35181000-35182600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:35181000-35182600	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr6:35181000-35182800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:35181000-35183000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:35181000-35183000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:35181200-35181600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:35181200-35181600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
25	chr6:35181200-35181600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:35181200-35181600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:35181200-35181600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
28	chr6:35181200-35181600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:35181200-35181600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:35181200-35181600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr6:35181200-35181600	Flanking Active TSS	Esophagus	oesophagus
32	chr6:35181200-35181600	Bivalent Enhancer	Fetal Thymus	thymus
33	chr6:35181200-35181600	Flanking Active TSS	Ovary	ovary
34	chr6:35181200-35181600	Enhancers	Pancreas	Pancrea
35	chr6:35181200-35181600	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
36	chr6:35181200-35181600	Flanking Active TSS	Right Atrium	heart
37	chr6:35181200-35181600	Bivalent/Poised TSS	HSMM	muscle
38	chr6:35181200-35181800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
39	chr6:35181200-35181800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
40	chr6:35181200-35181800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
41	chr6:35181200-35181800	Bivalent Enhancer	Spleen	Spleen
42	chr6:35181200-35181800	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr6:35181200-35182000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
44	chr6:35181200-35182000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:35181200-35182000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
46	chr6:35181200-35182000	Flanking Active TSS	Liver	Liver
47	chr6:35181200-35182000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr6:35181200-35182000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr6:35181200-35182000	Flanking Active TSS	Gastric	stomach
50	chr6:35181200-35182400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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