Variant report

Variant	rs3753668
Chromosome Location	chr1:226071754-226071755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:226071625-226072024	HepG2	liver:	n/a	n/a
2	CTCF	chr1:226071740-226071890	HepG2	liver:	n/a	n/a
3	CTCF	chr1:226071740-226071890	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:226071740-226071890	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr1:226071680-226071830	GM12874	blood:	n/a	n/a
6	CTCF	chr1:226071734-226071872	GM19239	blood:	n/a	n/a
7	RCOR1	chr1:226071711-226071795	K562	blood:	n/a	n/a
8	CTCF	chr1:226071716-226071884	GM12892	blood:	n/a	n/a
9	MAX	chr1:226071658-226071858	Hela-S3	cervix:	n/a	n/a
10	GTF2F1	chr1:226071686-226071845	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr1:226071660-226071930	A549	lung:	n/a	n/a
12	BRCA1	chr1:226071620-226071940	Hela-S3	cervix:	n/a	n/a
13	KAP1	chr1:226071651-226071929	K562	blood:	n/a	n/a
14	CTCF	chr1:226071430-226072178	HCT-116	colon:	n/a	n/a
15	RCOR1	chr1:226071748-226071829	K562	blood:	n/a	n/a
16	CTCF	chr1:226071660-226071810	GM12871	blood:	n/a	n/a
17	RAD21	chr1:226071713-226071936	HepG2	liver:	n/a	n/a
18	RAD21	chr1:226071658-226072042	MCF-7	breast:	n/a	n/a
19	MAZ	chr1:226071636-226071862	K562	blood:	n/a	chr1:226071652-226071662
20	ZNF143	chr1:226071751-226071761	GM12878	blood:	n/a	n/a
21	CTCF	chr1:226071730-226071895	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr1:226071673-226071891	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:226071700-226071850	GM12875	blood:	n/a	n/a
24	CTCF	chr1:226071701-226071875	HepG2	liver:	n/a	n/a
25	CTCF	chr1:226071722-226071885	MCF-7	breast:	n/a	n/a
26	YY1	chr1:226071689-226071818	K562	blood:	n/a	n/a
27	CTCF	chr1:226071700-226071850	HCT-116	colon:	n/a	n/a
28	RAD21	chr1:226071412-226072116	HCT-116	colon:	n/a	n/a
29	RCOR1	chr1:226071668-226071849	Hela-S3	cervix:	n/a	n/a
30	ELF1	chr1:226071616-226071838	K562	blood:	n/a	n/a
31	RAD21	chr1:226071640-226071929	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr1:226071664-226071953	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr1:226071700-226071850	GM12872	blood:	n/a	n/a
34	RAD21	chr1:226071621-226071873	HepG2	liver:	n/a	n/a
35	CTCF	chr1:226071751-226071872	GM19240	blood:	n/a	n/a
36	RAD21	chr1:226071414-226072105	HCT-116	colon:	n/a	n/a
37	POLR2A	chr1:226071641-226071864	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr1:226071662-226071944	GM12878	blood:	n/a	n/a
39	YY1	chr1:226071544-226071916	HCT-116	colon:	n/a	n/a
40	TBL1XR1	chr1:226071691-226071754	K562	blood:	n/a	n/a
41	POLR2A	chr1:226071502-226071921	HCT-116	colon:	n/a	n/a
42	CTCF	chr1:226071733-226071873	MCF-7	breast:	n/a	n/a
43	MAZ	chr1:226071618-226071849	Hela-S3	cervix:	n/a	chr1:226071652-226071662
44	POLR2A	chr1:226071653-226071867	K562	blood:	n/a	n/a
45	CTCF	chr1:226071700-226071850	GM12871	blood:	n/a	n/a
46	CBX3	chr1:226071508-226071960	K562	blood:	n/a	n/a
47	CTCF	chr1:226071735-226071874	GM12891	blood:	n/a	n/a
48	SMC3	chr1:226071646-226071844	GM12878	blood:	n/a	n/a
49	CTCF	chr1:226071742-226071900	GM12878	blood:	n/a	n/a
50	CTCF	chr1:226071751-226071882	MCF-7	breast:	n/a	n/a

No data

(count:13 , 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	chr1:225662424..225663252-chr1:226071421..226072025,2	MCF-7	breast:
4	chr1:226047047..226048850-chr1:226067848..226071913,3	MCF-7	breast:
5	chr1:226070165..226072280-chr1:226086600..226088627,2	K562	blood:
6	chr1:226070192..226076477-chr1:226076711..226082534,9	K562	blood:
7	chr1:226070563..226073306-chr1:226118336..226120549,2	K562	blood:
8	chr1:226054269..226057848-chr1:226069122..226072255,3	K562	blood:
9	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
10	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
11	chr1:226070971..226073106-chr1:226113461..226115401,2	MCF-7	breast:
12	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
13	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:

No data

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

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

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]
rs10915874	1.00[CEU][hapmap]
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]
rs1877726	0.83[LWK][hapmap];0.89[YRI][hapmap]
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	1.00[CEU][hapmap];1.00[TSI][hapmap];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]
rs360087	0.81[GIH][hapmap]
rs360089	0.81[GIH][hapmap]
rs3738050	0.90[EUR][1000 genomes]
rs3738051	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3753663	0.90[EUR][1000 genomes]
rs3753666	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3753670	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	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4149228	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4149230	0.90[EUR][1000 genomes]
rs45467394	0.84[EUR][1000 genomes]
rs4653437	0.81[YRI][hapmap]
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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226068600-226072000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:226069400-226071800	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:226070800-226072000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:226071000-226071800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr1:226071000-226073800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:226071000-226074200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:226071000-226076200	Weak transcription	Small Intestine	intestine
8	chr1:226071000-226076400	Weak transcription	Spleen	Spleen
9	chr1:226071000-226078600	Weak transcription	Lung	lung
10	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:226071200-226071800	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:226071200-226071800	Enhancers	Primary T cells from cord blood	blood
13	chr1:226071200-226071800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:226071200-226071800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:226071200-226071800	Enhancers	Brain Angular Gyrus	brain
16	chr1:226071200-226071800	Enhancers	Brain Substantia Nigra	brain
17	chr1:226071200-226071800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:226071200-226071800	Enhancers	Fetal Muscle Trunk	muscle
19	chr1:226071200-226071800	Enhancers	Placenta	Placenta
20	chr1:226071200-226071800	Bivalent Enhancer	Fetal Thymus	thymus
21	chr1:226071200-226071800	Enhancers	Right Ventricle	heart
22	chr1:226071200-226071800	Enhancers	GM12878-XiMat	blood
23	chr1:226071200-226071800	Enhancers	K562	blood
24	chr1:226071200-226072000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr1:226071200-226072000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:226071200-226072000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:226071200-226072000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:226071200-226072000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:226071200-226072000	Enhancers	Liver	Liver
30	chr1:226071200-226072000	Enhancers	Brain Hippocampus Middle	brain
31	chr1:226071200-226072000	Enhancers	Fetal Intestine Large	intestine
32	chr1:226071200-226072000	Enhancers	Pancreas	Pancrea
33	chr1:226071200-226072000	Enhancers	Stomach Mucosa	stomach
34	chr1:226071200-226072800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:226071200-226073000	Weak transcription	Right Atrium	heart
36	chr1:226071200-226073000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:226071200-226073800	Weak transcription	Thymus	Thymus
38	chr1:226071200-226074600	Weak transcription	Fetal Lung	lung
39	chr1:226071200-226075000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:226071200-226075400	Weak transcription	Ovary	ovary
41	chr1:226071200-226076200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:226071200-226076200	Weak transcription	Fetal Kidney	kidney
43	chr1:226071200-226076200	Weak transcription	A549	lung
44	chr1:226071200-226078200	Weak transcription	Gastric	stomach
45	chr1:226071200-226078200	Weak transcription	HMEC	breast
46	chr1:226071400-226071800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr1:226071400-226071800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:226071400-226071800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:226071400-226071800	Enhancers	Left Ventricle	heart
50	chr1:226071400-226071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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