Variant report

Variant	rs3753794
Chromosome Location	chr1:86045642-86045643
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	POLR2A	chr1:86045313-86051202	ProgFib	skin:	n/a	n/a
2	POLR2A	chr1:86041793-86051199	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:86045276-86045858	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr1:86045223-86048449	H1-hESC	embryonic stem cell:	n/a	n/a
5	NFIC	chr1:86045561-86049147	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:86041833-86052222	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:86041771-86051250	HUVEC	blood vessel:	n/a	n/a
8	GATA3	chr1:86045616-86047524	A549	lung:	n/a	chr1:86046062-86046071
9	CHD1	chr1:86041753-86052318	IMR90	lung:	n/a	chr1:86046866-86046876 chr1:86046027-86046037 chr1:86044526-86044536
10	POLR2A	chr1:86045283-86045710	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:86041854-86051160	PANC-1	pancreas:	n/a	n/a
12	SIN3A	chr1:86045288-86048435	H1-hESC	embryonic stem cell:	n/a	chr1:86046470-86046479 chr1:86046767-86046778
13	POLR2A	chr1:86041016-86051875	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:86045361-86051797	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F6	chr1:86045171-86045657	H1-hESC	embryonic stem cell:	n/a	chr1:86045440-86045452
16	POLR2A	chr1:86044532-86052365	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr1:86045218-86045643	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD1	chr1:86044932-86050997	H1-hESC	embryonic stem cell:	n/a	chr1:86046866-86046876 chr1:86046027-86046037
19	POLR2A	chr1:86045216-86045885	PFSK-1	brain:	n/a	n/a
20	SIN3AK20	chr1:86045201-86047524	PANC-1	pancreas:	n/a	n/a
21	FOXA2	chr1:86045296-86045692	A549	lung:	n/a	n/a
22	POLR2A	chr1:86041739-86051909	PANC-1	pancreas:	n/a	n/a
23	TAF7	chr1:86045208-86051049	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3AK20	chr1:86045325-86045661	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr1:86041763-86045645	HUVEC	blood vessel:	n/a	n/a
26	FOS	chr1:86045271-86045657	HUVEC	blood vessel:	n/a	chr1:86045439-86045448
27	TCF7L2	chr1:86045483-86049012	PANC-1	pancreas:	n/a	chr1:86047350-86047360 chr1:86045792-86045801
28	POLR2A	chr1:86041675-86051128	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:86040817-86051935	IMR90	lung:	n/a	n/a
30	POLR2A	chr1:86045177-86045655	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:86044508..86046201-chr1:86070309..86072884,2	K562	blood:
2	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
3	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
4	chr1:85930091..85932037-chr1:86045511..86048058,4	MCF-7	breast:
5	chr1:85929622..85931400-chr1:86044914..86046491,2	MCF-7	breast:
6	chr1:85958709..85962572-chr1:86044730..86049172,10	MCF-7	breast:
7	chr1:85959814..85963220-chr1:86043447..86048399,5	MCF-7	breast:
8	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
9	chr1:86043937..86050216-chr1:86058297..86066765,12	K562	blood:
10	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
CYR61	TF binding region
DDAH1	TF binding region
ENSG00000272691	TF binding region
ENSG00000117174	Chromatin interaction
ENSG00000230285	Chromatin interaction
ENSG00000199934	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10493772	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12034319	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753793	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3753795	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4370804	0.82[EUR][1000 genomes]
rs721471	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9658595	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86041800-86047800	Active TSS	Aorta	Aorta
2	chr1:86043000-86046600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:86043600-86045800	Weak transcription	K562	blood
4	chr1:86043800-86045800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:86044000-86045800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:86044000-86045800	Enhancers	Fetal Lung	lung
7	chr1:86044000-86045800	Weak transcription	Gastric	stomach
8	chr1:86044000-86045800	Weak transcription	Lung	lung
9	chr1:86044000-86045800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:86044200-86045800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr1:86044200-86045800	Enhancers	Fetal Heart	heart
12	chr1:86044200-86045800	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr1:86044400-86045800	Weak transcription	Colonic Mucosa	Colon
14	chr1:86044600-86046200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:86044600-86046200	Flanking Active TSS	Osteobl	bone
16	chr1:86045000-86045800	Weak transcription	Liver	Liver
17	chr1:86045000-86047200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr1:86045200-86045800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:86045200-86045800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:86045200-86045800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:86045200-86045800	Enhancers	Brain Cingulate Gyrus	brain
22	chr1:86045200-86045800	Enhancers	Placenta	Placenta
23	chr1:86045200-86045800	Enhancers	Left Ventricle	heart
24	chr1:86045200-86045800	Enhancers	Pancreas	Pancrea
25	chr1:86045200-86045800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
26	chr1:86045200-86046200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:86045200-86046200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr1:86045200-86046200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:86045200-86046200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:86045200-86046600	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr1:86045200-86047000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:86045200-86047400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:86045200-86047600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:86045200-86047600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:86045200-86048600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr1:86045400-86045800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:86045400-86045800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:86045400-86045800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:86045400-86045800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
40	chr1:86045400-86045800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr1:86045400-86045800	Bivalent Enhancer	Fetal Brain Male	brain
42	chr1:86045400-86045800	Bivalent Enhancer	Small Intestine	intestine
43	chr1:86045400-86045800	Flanking Active TSS	NHEK	skin
44	chr1:86045400-86046000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr1:86045400-86046000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr1:86045400-86046000	Flanking Active TSS	Fetal Stomach	stomach
47	chr1:86045400-86046400	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr1:86045400-86046600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:86045400-86046600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr1:86045400-86046600	Active TSS	Esophagus	oesophagus

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