Variant report

Variant	rs3753666
Chromosome Location	chr1:226071570-226071571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:226071540-226071690	GM06990	blood:	n/a	n/a
2	CTCF	chr1:226071430-226072178	HCT-116	colon:	n/a	n/a
3	RAD21	chr1:226071412-226072116	HCT-116	colon:	n/a	n/a
4	RAD21	chr1:226071414-226072105	HCT-116	colon:	n/a	n/a
5	YY1	chr1:226071544-226071916	HCT-116	colon:	n/a	n/a
6	POLR2A	chr1:226071502-226071921	HCT-116	colon:	n/a	n/a
7	CBX3	chr1:226071508-226071960	K562	blood:	n/a	n/a
8	POLR2A	chr1:226071519-226071885	HCT-116	colon:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226053217..226056086-chr1:226069002..226071584,2	MCF-7	breast:
2	chr1:225964533..225968744-chr1:226068261..226071590,3	MCF-7	breast:
3	chr1:226070080..226072229-chr1:226145455..226147029,2	K562	blood:
4	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:
5	chr1:226069198..226071720-chr1:226149361..226151916,2	MCF-7	breast:
6	chr1:225662424..225663252-chr1:226071421..226072025,2	MCF-7	breast:
7	chr1:226047047..226048850-chr1:226067848..226071913,3	MCF-7	breast:
8	chr1:226070165..226072280-chr1:226086600..226088627,2	K562	blood:
9	chr1:226067837..226071624-chr1:226184531..226189088,6	K562	blood:
10	chr1:226070192..226076477-chr1:226076711..226082534,9	K562	blood:
11	chr1:226070563..226073306-chr1:226118336..226120549,2	K562	blood:
12	chr1:226054269..226057848-chr1:226069122..226072255,3	K562	blood:
13	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
14	chr1:225660989..225663497-chr1:226070471..226072090,2	K562	blood:
15	chr1:226070971..226073106-chr1:226113461..226115401,2	MCF-7	breast:
16	chr1:226066440..226072029-chr1:226106315..226113044,10	MCF-7	breast:
17	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM63A	TF binding region
ENSG00000143811	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000213032	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000196187	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	0.92[EUR][1000 genomes]
rs10915874	1.00[CEU][hapmap]
rs12061043	0.92[EUR][1000 genomes]
rs12071072	0.92[EUR][1000 genomes]
rs12071104	0.92[EUR][1000 genomes]
rs12074209	0.92[EUR][1000 genomes]
rs12074247	0.92[EUR][1000 genomes]
rs12075664	0.92[EUR][1000 genomes]
rs2236143	0.90[EUR][1000 genomes]
rs2271544	0.97[EUR][1000 genomes]
rs2292556	0.92[EUR][1000 genomes]
rs2292559	0.92[EUR][1000 genomes]
rs2292561	0.92[EUR][1000 genomes]
rs2292568	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs28384446	0.95[EUR][1000 genomes]
rs28384447	0.88[EUR][1000 genomes]
rs28384448	0.97[EUR][1000 genomes]
rs28384449	0.97[EUR][1000 genomes]
rs3738050	0.92[EUR][1000 genomes]
rs3738051	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3753663	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3753668	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3753670	0.92[EUR][1000 genomes]
rs3766935	0.92[EUR][1000 genomes]
rs3766936	0.92[EUR][1000 genomes]
rs3766937	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3766940	0.97[EUR][1000 genomes]
rs3766941	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3806257	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3806258	0.92[EUR][1000 genomes]
rs41310561	0.92[EUR][1000 genomes]
rs4149227	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4149228	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4149230	0.92[EUR][1000 genomes]
rs45467394	0.87[EUR][1000 genomes]
rs56231004	0.92[EUR][1000 genomes]
rs56325807	0.92[EUR][1000 genomes]
rs57095220	0.92[EUR][1000 genomes]
rs57932384	0.92[EUR][1000 genomes]
rs59728172	0.92[EUR][1000 genomes]
rs60847271	0.97[EUR][1000 genomes]
rs60943392	0.92[EUR][1000 genomes]
rs61033712	0.92[EUR][1000 genomes]
rs61227102	0.92[EUR][1000 genomes]
rs61295362	0.92[EUR][1000 genomes]
rs6664740	0.92[EUR][1000 genomes]
rs74150536	0.92[EUR][1000 genomes]
rs7514448	0.92[EUR][1000 genomes]
rs7516538	0.92[EUR][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:74 , 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	chr1:226069400-226071600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:226069400-226071600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:226069400-226071600	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr1:226069400-226071800	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:226070400-226071600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:226070800-226072000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr1:226071000-226071600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:226071000-226071800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr1:226071000-226073800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:226071000-226074200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:226071000-226076200	Weak transcription	Small Intestine	intestine
13	chr1:226071000-226076400	Weak transcription	Spleen	Spleen
14	chr1:226071000-226078600	Weak transcription	Lung	lung
15	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:226071200-226071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:226071200-226071600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:226071200-226071600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:226071200-226071600	Active TSS	Primary B cells from cord blood	blood
20	chr1:226071200-226071600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:226071200-226071600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:226071200-226071600	Enhancers	Adipose Nuclei	Adipose
23	chr1:226071200-226071600	Active TSS	Colonic Mucosa	Colon
24	chr1:226071200-226071600	Enhancers	Colon Smooth Muscle	Colon
25	chr1:226071200-226071600	Weak transcription	Esophagus	oesophagus
26	chr1:226071200-226071600	Enhancers	NHDF-Ad	bronchial
27	chr1:226071200-226071800	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:226071200-226071800	Enhancers	Primary T cells from cord blood	blood
29	chr1:226071200-226071800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:226071200-226071800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:226071200-226071800	Enhancers	Brain Angular Gyrus	brain
32	chr1:226071200-226071800	Enhancers	Brain Substantia Nigra	brain
33	chr1:226071200-226071800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:226071200-226071800	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:226071200-226071800	Enhancers	Placenta	Placenta
36	chr1:226071200-226071800	Bivalent Enhancer	Fetal Thymus	thymus
37	chr1:226071200-226071800	Enhancers	Right Ventricle	heart
38	chr1:226071200-226071800	Enhancers	GM12878-XiMat	blood
39	chr1:226071200-226071800	Enhancers	K562	blood
40	chr1:226071200-226072000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:226071200-226072000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:226071200-226072000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:226071200-226072000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:226071200-226072000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:226071200-226072000	Enhancers	Liver	Liver
46	chr1:226071200-226072000	Enhancers	Brain Hippocampus Middle	brain
47	chr1:226071200-226072000	Enhancers	Fetal Intestine Large	intestine
48	chr1:226071200-226072000	Enhancers	Pancreas	Pancrea
49	chr1:226071200-226072000	Enhancers	Stomach Mucosa	stomach
50	chr1:226071200-226072800	Weak transcription	Primary monocytes fromperipheralblood	blood

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