Variant report

Variant	rs3795712
Chromosome Location	chr1:45206495-45206496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45205245..45207359-chr1:45265556..45268016,2	MCF-7	breast:
2	chr1:45205752..45207345-chr1:45476946..45478551,2	K562	blood:
3	chr1:45203850..45207286-chr1:45238882..45241584,6	MCF-7	breast:
4	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
5	chr1:45205081..45206794-chr1:45478593..45481166,2	K562	blood:
6	chr1:45205816..45209212-chr1:45986070..45988878,3	K562	blood:
7	chr1:45204996..45206772-chr1:45226218..45229043,2	MCF-7	breast:
8	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
9	chr1:45193557..45198509-chr1:45202622..45207012,16	MCF-7	breast:
10	chr1:45204011..45207083-chr1:45240823..45243671,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225721	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200913	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10159318	1.00[JPT][hapmap]
rs11211052	1.00[JPT][hapmap]
rs12057238	0.83[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs12057414	0.91[ASN][1000 genomes]
rs12093313	0.92[CHD][hapmap]
rs12402781	0.83[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs12404160	0.80[ASN][1000 genomes]
rs12407290	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12407627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16832301	0.88[CHD][hapmap]
rs17390328	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs17391430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17392632	0.92[CHD][hapmap]
rs17883304	0.86[ASN][1000 genomes]
rs17885815	0.80[ASN][1000 genomes]
rs2983715	0.94[CEU][hapmap]
rs3738248	1.00[JPT][hapmap]
rs3795715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806398	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3889352	0.90[JPT][hapmap]
rs3923304	0.86[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4082644	0.92[CHD][hapmap]
rs41269079	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4520451	0.80[ASN][1000 genomes]
rs4565758	0.86[ASN][1000 genomes]
rs55703843	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58532407	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58603818	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59895800	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60452778	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60766209	0.91[EUR][1000 genomes]
rs608649	0.96[CHD][hapmap];1.00[JPT][hapmap]
rs72671996	0.80[EUR][1000 genomes]
rs72674017	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674023	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519592	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
7	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
8	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
9	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3795712	CDC20	cis	cerebellum	SCAN
rs3795712	C1orf84	cis	parietal	SCAN
rs3795712	NASP	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45203800-45206600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:45204800-45206600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr1:45204800-45206600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:45204800-45206600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:45204800-45206600	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:45204800-45206800	Active TSS	NHLF	lung
7	chr1:45204800-45207000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:45204800-45207000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:45204800-45207200	Active TSS	GM12878-XiMat	blood
10	chr1:45204800-45207400	Active TSS	HSMM	muscle
11	chr1:45205000-45206600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:45205000-45206600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:45205000-45206600	Active TSS	A549	lung
14	chr1:45205000-45206800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:45205200-45206600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:45205600-45206600	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:45205600-45206600	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr1:45205600-45206800	Flanking Active TSS	HUVEC	blood vessel
19	chr1:45205600-45207200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:45205800-45206600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:45205800-45206600	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr1:45205800-45206600	Flanking Active TSS	Fetal Heart	heart
23	chr1:45205800-45206600	Flanking Active TSS	Osteobl	bone
24	chr1:45205800-45206800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:45205800-45206800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr1:45205800-45206800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:45205800-45206800	Flanking Active TSS	HMEC	breast
28	chr1:45205800-45240600	Weak transcription	Ovary	ovary
29	chr1:45206000-45206600	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:45206000-45206600	Active TSS	Fetal Muscle Trunk	muscle
31	chr1:45206000-45206800	Flanking Active TSS	NHDF-Ad	bronchial
32	chr1:45206000-45223400	Weak transcription	Lung	lung
33	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
34	chr1:45206200-45206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:45206200-45206600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:45206200-45206600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:45206200-45206600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:45206200-45206600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:45206200-45206600	Active TSS	Fetal Brain Female	brain
40	chr1:45206200-45206600	Flanking Active TSS	Dnd41	blood
41	chr1:45206200-45206800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:45206200-45206800	Active TSS	Fetal Brain Male	brain
43	chr1:45206200-45206800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:45206200-45206800	Flanking Active TSS	Hela-S3	cervix
45	chr1:45206200-45206800	Flanking Active TSS	HepG2	liver
46	chr1:45206200-45206800	Flanking Active TSS	NHEK	skin
47	chr1:45206200-45207000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:45206200-45213400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:45206200-45218400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:45206200-45218800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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