Variant report

Variant	rs3753670
Chromosome Location	chr1:226072090-226072091
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:226071430-226072178	HCT-116	colon:	n/a	n/a
2	RAD21	chr1:226071412-226072116	HCT-116	colon:	n/a	n/a
3	RAD21	chr1:226071414-226072105	HCT-116	colon:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226070080..226072229-chr1:226145455..226147029,2	K562	blood:
2	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:
3	chr1:226070165..226072280-chr1:226086600..226088627,2	K562	blood:
4	chr1:226070192..226076477-chr1:226076711..226082534,9	K562	blood:
5	chr1:226070563..226073306-chr1:226118336..226120549,2	K562	blood:
6	chr1:226054269..226057848-chr1:226069122..226072255,3	K562	blood:
7	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
8	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
9	chr1:226070971..226073106-chr1:226113461..226115401,2	MCF-7	breast:
10	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000196187	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000243709	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10047091	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10158952	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12061043	1.00[EUR][1000 genomes]
rs12071072	1.00[EUR][1000 genomes]
rs12071104	1.00[EUR][1000 genomes]
rs12074209	1.00[EUR][1000 genomes]
rs12074247	1.00[EUR][1000 genomes]
rs12075664	0.90[EUR][1000 genomes]
rs2236143	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271544	0.95[EUR][1000 genomes]
rs2292556	0.90[EUR][1000 genomes]
rs2292559	0.90[EUR][1000 genomes]
rs2292561	0.90[EUR][1000 genomes]
rs2292568	0.87[EUR][1000 genomes]
rs28384446	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28384447	0.86[EUR][1000 genomes]
rs28384448	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28384449	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738050	0.90[EUR][1000 genomes]
rs3738051	0.90[EUR][1000 genomes]
rs3753663	0.90[EUR][1000 genomes]
rs3753666	0.92[EUR][1000 genomes]
rs3753668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766935	0.90[EUR][1000 genomes]
rs3766936	0.90[EUR][1000 genomes]
rs3766937	0.90[EUR][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806257	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806258	1.00[EUR][1000 genomes]
rs41310561	1.00[EUR][1000 genomes]
rs4149227	0.87[EUR][1000 genomes]
rs4149228	0.90[EUR][1000 genomes]
rs4149230	0.90[EUR][1000 genomes]
rs45467394	0.84[EUR][1000 genomes]
rs56231004	1.00[EUR][1000 genomes]
rs56325807	0.90[EUR][1000 genomes]
rs57095220	0.90[EUR][1000 genomes]
rs57932384	0.90[EUR][1000 genomes]
rs59728172	0.90[EUR][1000 genomes]
rs60847271	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60943392	0.90[EUR][1000 genomes]
rs61033712	0.90[EUR][1000 genomes]
rs61227102	0.90[EUR][1000 genomes]
rs61295362	0.90[EUR][1000 genomes]
rs6664740	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74150536	0.90[EUR][1000 genomes]
rs7514448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516538	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3354874	chr1:226069354-226072202	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226073800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:226071000-226074200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:226071000-226076200	Weak transcription	Small Intestine	intestine
4	chr1:226071000-226076400	Weak transcription	Spleen	Spleen
5	chr1:226071000-226078600	Weak transcription	Lung	lung
6	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:226071200-226072800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:226071200-226073000	Weak transcription	Right Atrium	heart
9	chr1:226071200-226073000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:226071200-226073800	Weak transcription	Thymus	Thymus
11	chr1:226071200-226074600	Weak transcription	Fetal Lung	lung
12	chr1:226071200-226075000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:226071200-226075400	Weak transcription	Ovary	ovary
14	chr1:226071200-226076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:226071200-226076200	Weak transcription	Fetal Kidney	kidney
16	chr1:226071200-226076200	Weak transcription	A549	lung
17	chr1:226071200-226078200	Weak transcription	Gastric	stomach
18	chr1:226071200-226078200	Weak transcription	HMEC	breast
19	chr1:226071400-226075000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:226071600-226074200	Weak transcription	NHDF-Ad	bronchial
21	chr1:226071600-226076800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:226071800-226073800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:226071800-226074000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:226071800-226074000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:226071800-226074200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:226071800-226074400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:226071800-226074400	Weak transcription	Colonic Mucosa	Colon
28	chr1:226071800-226074400	Weak transcription	Esophagus	oesophagus
29	chr1:226071800-226074400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:226071800-226074600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:226071800-226076000	Weak transcription	Right Ventricle	heart
32	chr1:226071800-226076400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:226071800-226076400	Weak transcription	Placenta	Placenta
34	chr1:226071800-226076800	Weak transcription	K562	blood
35	chr1:226071800-226078800	Weak transcription	Primary T cells from cord blood	blood
36	chr1:226072000-226073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:226072000-226073000	Weak transcription	HepG2	liver
38	chr1:226072000-226073200	Weak transcription	Liver	Liver
39	chr1:226072000-226074000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:226072000-226074200	Weak transcription	Fetal Intestine Small	intestine
41	chr1:226072000-226074200	Weak transcription	Pancreas	Pancrea
42	chr1:226072000-226074200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:226072000-226074200	Weak transcription	Stomach Mucosa	stomach
44	chr1:226072000-226075200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:226072000-226076800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:226072000-226081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:226072000-226081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:226072000-226082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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