Variant report

Variant	rs3827758
Chromosome Location	chr2:113414986-113414987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113413978-113415335	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr2:113414112-113415318	HL-60	blood:	n/a	n/a
3	CUX1	chr2:113414970-113415027	K562	blood:	n/a	n/a
4	POLR2A	chr2:113411600-113418968	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:113411634-113419051	K562	blood:	n/a	n/a
6	POLR2A	chr2:113414128-113415966	PBDE	blood:	n/a	n/a
7	POLR2A	chr2:113414072-113417578	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:113413981-113415070	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:113413996-113416086	K562	blood:	n/a	n/a
10	POLR2A	chr2:113401765-113425023	U87	brain:	n/a	n/a
11	POLR2A	chr2:113412613-113416005	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:113414148-113417968	K562	blood:	n/a	n/a
13	POLR2A	chr2:113413925-113417501	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:113414152-113415012	HepG2	liver:	n/a	n/a
15	HEY1	chr2:113414107-113415931	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:113414397-113415318	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr2:113413986-113419936	U87	brain:	n/a	n/a
18	POLR2A	chr2:113414179-113415359	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:113412120-113418364	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:113401943-113419910	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr2:113413840-113417746	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr2:113414091-113417438	K562	blood:	n/a	n/a
23	POLR2A	chr2:113413955-113415155	K562	blood:	n/a	n/a
24	POLR2A	chr2:113414051-113415102	K562	blood:	n/a	n/a
25	POLR2A	chr2:113401765-113425014	U87	brain:	n/a	n/a
26	PML	chr2:113413966-113416283	K562	blood:	n/a	n/a
27	POLR2A	chr2:113414930-113415328	HCT-116	colon:	n/a	n/a
28	POLR2A	chr2:113411663-113418887	A549	lung:	n/a	n/a
29	POLR2A	chr2:113414082-113417008	IMR90	lung:	n/a	n/a
30	POLR2A	chr2:113414142-113415135	GM12891	blood:	n/a	n/a

No data

Variant related genes	Relation type
SLC20A1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10167360	0.95[ASN][1000 genomes]
rs10184339	0.86[ASN][1000 genomes]
rs1053652	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10758	0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10779885	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11123146	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11680181	0.86[JPT][hapmap]
rs11889567	0.95[ASN][1000 genomes]
rs12467747	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475403	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12479380	0.81[CEU][hapmap]
rs12612089	0.97[ASN][1000 genomes]
rs12612238	0.95[ASN][1000 genomes]
rs12618806	0.95[ASN][1000 genomes]
rs17515708	0.84[ASN][1000 genomes]
rs17515715	0.84[ASN][1000 genomes]
rs2048873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34282612	0.83[ASN][1000 genomes]
rs4261730	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4368335	0.81[CEU][hapmap]
rs4848288	0.83[JPT][hapmap]
rs4849086	0.83[CHB][hapmap]
rs4849091	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4849097	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57033895	0.86[EUR][1000 genomes]
rs58662040	0.86[ASN][1000 genomes]
rs58797970	0.85[EUR][1000 genomes]
rs60372418	0.99[ASN][1000 genomes]
rs6542074	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6705487	0.89[CHB][hapmap]
rs6725228	0.81[ASN][1000 genomes]
rs72823516	0.95[ASN][1000 genomes]
rs7371700	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9308674	0.94[ASN][1000 genomes]
rs9308675	0.95[ASN][1000 genomes]
rs9308676	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113404800-113416200	Weak transcription	Ovary	ovary
2	chr2:113404800-113416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:113405000-113416200	Weak transcription	Aorta	Aorta
4	chr2:113405000-113416400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:113405000-113423200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:113405200-113419000	Weak transcription	Stomach Mucosa	stomach
7	chr2:113405200-113423200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr2:113405200-113423800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr2:113405400-113422600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:113405400-113423200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:113405400-113423200	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:113405600-113422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:113405800-113422600	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:113406000-113419600	Strong transcription	Fetal Lung	lung
15	chr2:113406000-113423000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:113406200-113423400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:113406200-113423400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:113406200-113423600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:113406200-113424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:113406400-113423000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr2:113406400-113423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:113406400-113423200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:113406800-113423200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:113407000-113415200	Strong transcription	A549	lung
25	chr2:113407000-113416800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:113407000-113417000	Weak transcription	Fetal Brain Male	brain
27	chr2:113407000-113420600	Strong transcription	Adipose Nuclei	Adipose
28	chr2:113407000-113423000	Strong transcription	NHDF-Ad	bronchial
29	chr2:113407000-113423200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:113407000-113423200	Strong transcription	Fetal Thymus	thymus
31	chr2:113407000-113423200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:113407000-113423400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:113407000-113423400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr2:113407200-113415600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:113407200-113417200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:113407400-113417000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:113407400-113417200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:113407400-113419400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr2:113407400-113422800	Strong transcription	HSMMtube	muscle
40	chr2:113407600-113415600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:113407600-113417200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:113407600-113422200	Strong transcription	HSMM	muscle
43	chr2:113407600-113422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:113407600-113422800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:113407800-113415400	Strong transcription	NH-A	brain
46	chr2:113407800-113415600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:113407800-113415600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:113407800-113415800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:113408200-113417200	Strong transcription	Primary T cells from cord blood	blood
50	chr2:113408200-113423000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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