Variant report

Variant	rs7748940
Chromosome Location	chr6:119594540-119594541
allele	C/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	GATA3	chr6:119594487-119596069	SK-N-SH	brain:	n/a	chr6:119595700-119595707
2	POLR2A	chr6:119593866-119595281	K562	blood:	n/a	n/a
3	EP300	chr6:119594426-119596136	SK-N-SH	brain:	n/a	chr6:119596042-119596056
4	TCF12	chr6:119594527-119595940	SK-N-SH	brain:	n/a	chr6:119595255-119595263

Variant related genes	Relation type
ENSG00000216316	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs17442217	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17442238	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17442343	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17442478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17442505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17514202	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17526989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17527003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17527153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17536339	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17619366	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2038768	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3798611	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56320899	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56926474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6569064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6911026	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6917219	0.86[AFR][1000 genomes]
rs6923206	1.00[YRI][hapmap]
rs6926266	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6933973	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6941142	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6941514	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73767443	0.84[AFR][1000 genomes]
rs73769010	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73769011	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73769020	0.92[AFR][1000 genomes]
rs73769050	0.81[AFR][1000 genomes]
rs7740521	1.00[EUR][1000 genomes]
rs7740969	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7743309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7757386	0.92[AFR][1000 genomes]
rs7763451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7763610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7767940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7769071	0.86[AFR][1000 genomes]
rs7769133	0.86[AFR][1000 genomes]
rs9481896	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9481897	0.86[AFR][1000 genomes]
rs9481899	0.86[AFR][1000 genomes]
rs9481905	0.81[AFR][1000 genomes]
rs9481906	0.86[AFR][1000 genomes]
rs9489640	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9489641	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9489642	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9489643	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9489644	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489647	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489652	0.88[EUR][1000 genomes]
rs9489655	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489656	0.86[AFR][1000 genomes]
rs9489657	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489658	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489659	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489660	0.86[AFR][1000 genomes]
rs9489666	0.86[AFR][1000 genomes]
rs9489684	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv886570	chr6:119450888-119600556	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1017507	chr6:119465981-119664949	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119558800-119602000	Weak transcription	Gastric	stomach
2	chr6:119589200-119598600	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:119589200-119611000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:119590600-119621800	Weak transcription	Placenta	Placenta
5	chr6:119590800-119617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:119590800-119626600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:119591000-119599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:119591000-119599800	Weak transcription	Lung	lung
9	chr6:119591000-119600600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:119591000-119624200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:119591200-119602000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:119591200-119604600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:119591400-119601400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:119591600-119595200	ZNF genes & repeats	K562	blood
15	chr6:119591800-119597000	Weak transcription	Fetal Kidney	kidney
16	chr6:119592000-119602200	Weak transcription	Left Ventricle	heart
17	chr6:119592000-119604200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:119592200-119594600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:119592200-119594600	Weak transcription	NHDF-Ad	bronchial
20	chr6:119592200-119597400	Weak transcription	NHLF	lung
21	chr6:119592200-119622200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:119592400-119594600	Weak transcription	Adipose Nuclei	Adipose
23	chr6:119592400-119596800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:119592400-119597200	Weak transcription	Liver	Liver
25	chr6:119592400-119601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:119592400-119604800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:119592400-119610600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:119592400-119620800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:119592400-119633600	Weak transcription	Primary T cells from cord blood	blood
30	chr6:119592600-119622200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:119592600-119627200	Weak transcription	Dnd41	blood
32	chr6:119593000-119599800	Weak transcription	Aorta	Aorta
33	chr6:119593000-119622200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:119593000-119624800	Weak transcription	Fetal Thymus	thymus
35	chr6:119593000-119626800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:119593200-119594600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:119593200-119604600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:119593400-119595000	Enhancers	Fetal Lung	lung
39	chr6:119593400-119595600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr6:119593600-119594800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:119593600-119596800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:119593800-119596800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:119593800-119597000	Weak transcription	Primary B cells from cord blood	blood
44	chr6:119594000-119596000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:119594200-119605000	Strong transcription	HepG2	liver
46	chr6:119594400-119596000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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