Variant report

Variant	rs3753795
Chromosome Location	chr1:86045104-86045105
allele	A/G
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	chr1:86041793-86051199	HUVEC	blood vessel:	n/a	n/a
2	MAZ	chr1:86041801-86045145	IMR90	lung:	n/a	chr1:86043557-86043566 chr1:86042284-86042294 chr1:86044528-86044538
3	JUN	chr1:86044866-86045239	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:86041833-86052222	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr1:86041771-86051250	HUVEC	blood vessel:	n/a	n/a
6	CHD1	chr1:86041753-86052318	IMR90	lung:	n/a	chr1:86046866-86046876 chr1:86046027-86046037 chr1:86044526-86044536
7	POLR2A	chr1:86041854-86051160	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:86041016-86051875	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:86044532-86052365	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD1	chr1:86044932-86050997	H1-hESC	embryonic stem cell:	n/a	chr1:86046866-86046876 chr1:86046027-86046037
11	POLR2A	chr1:86041739-86051909	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr1:86045032-86045133	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:86041763-86045645	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:86041675-86051128	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:86040817-86051935	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:86044508..86046201-chr1:86070309..86072884,2	K562	blood:
2	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
3	chr1:85929622..85931400-chr1:86044914..86046491,2	MCF-7	breast:
4	chr1:85958709..85962572-chr1:86044730..86049172,10	MCF-7	breast:
5	chr1:85959814..85963220-chr1:86043447..86048399,5	MCF-7	breast:
6	chr1:86043937..86050216-chr1:86058297..86066765,12	K562	blood:
7	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
ENSG00000153904	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000230285	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10493772	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs10873708	0.82[CEU][hapmap]
rs12034319	0.85[ASN][1000 genomes]
rs3753793	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753794	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs721471	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753795	CLCA2	cis	cerebellum	SCAN
rs3753795	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86041600-86045200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:86041800-86047800	Active TSS	Aorta	Aorta
3	chr1:86042400-86045200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:86043000-86046600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:86043400-86045200	Weak transcription	Hela-S3	cervix
6	chr1:86043400-86045400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:86043600-86045800	Weak transcription	K562	blood
8	chr1:86043800-86045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:86043800-86045400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr1:86043800-86045400	Weak transcription	Esophagus	oesophagus
11	chr1:86043800-86045800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:86044000-86045200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:86044000-86045200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:86044000-86045200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:86044000-86045200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:86044000-86045200	Bivalent Enhancer	Fetal Brain Male	brain
17	chr1:86044000-86045200	Weak transcription	Pancreas	Pancrea
18	chr1:86044000-86045400	Enhancers	NHEK	skin
19	chr1:86044000-86045600	Weak transcription	Psoas Muscle	Psoas
20	chr1:86044000-86045800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:86044000-86045800	Enhancers	Fetal Lung	lung
22	chr1:86044000-86045800	Weak transcription	Gastric	stomach
23	chr1:86044000-86045800	Weak transcription	Lung	lung
24	chr1:86044000-86045800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:86044200-86045200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:86044200-86045200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:86044200-86045200	Weak transcription	Left Ventricle	heart
28	chr1:86044200-86045200	Enhancers	HMEC	breast
29	chr1:86044200-86045400	Enhancers	Colon Smooth Muscle	Colon
30	chr1:86044200-86045800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr1:86044200-86045800	Enhancers	Fetal Heart	heart
32	chr1:86044200-86045800	Bivalent Enhancer	Fetal Intestine Small	intestine
33	chr1:86044400-86045200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:86044400-86045200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr1:86044400-86045200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:86044400-86045200	Enhancers	Adipose Nuclei	Adipose
37	chr1:86044400-86045200	Weak transcription	Ovary	ovary
38	chr1:86044400-86045200	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:86044400-86045200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:86044400-86045200	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:86044400-86045200	Bivalent Enhancer	HepG2	liver
42	chr1:86044400-86045400	Enhancers	Fetal Muscle Leg	muscle
43	chr1:86044400-86045400	Enhancers	Fetal Stomach	stomach
44	chr1:86044400-86045400	Enhancers	Right Atrium	heart
45	chr1:86044400-86045600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:86044400-86045800	Weak transcription	Colonic Mucosa	Colon
47	chr1:86044600-86045200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:86044600-86045200	Enhancers	Right Ventricle	heart
49	chr1:86044600-86045400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr1:86044600-86045400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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