Variant report

Variant	rs35201844
Chromosome Location	chr3:49756212-49756213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49754469-49762505	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49755910-49757390	GM10847	blood:	n/a	n/a
3	POLR2A	chr3:49752450-49757371	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49755286-49762590	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr3:49755774-49757528	GM12878	blood:	n/a	n/a
6	E2F6	chr3:49755797-49757250	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:49755289-49757590	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:49756201-49757388	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:49754970-49763587	HepG2	liver:	n/a	n/a
10	PML	chr3:49755918-49757599	GM12878	blood:	n/a	n/a
11	MAX	chr3:49756045-49757399	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:49755962-49757476	H1-neurons	neurons:	n/a	n/a
13	NFATC1	chr3:49756004-49757550	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49755636-49757470	GM12878	blood:	n/a	n/a
15	GABPA	chr3:49756002-49757398	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr3:49756111-49757488	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:49755663-49757489	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr3:49754039-49757529	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr3:49755382-49762475	MCF-7	breast:	n/a	n/a
20	CCNT2	chr3:49756025-49757139	K562	blood:	n/a	n/a
21	CHD2	chr3:49755977-49757382	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:49756116-49757487	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr3:49756132-49756517	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:49756040-49757345	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:49754800-49756322	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr3:49751816-49757616	U87	brain:	n/a	n/a
27	MTA3	chr3:49755358-49757543	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:49756191-49757473	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:49756046-49756397	A549	lung:	n/a	n/a
30	CEBPB	chr3:49756079-49756300	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:49755367-49758782	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:49755399-49757458	GM18505	blood:	n/a	n/a
33	POLR2A	chr3:49755765-49757529	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:49755963-49757336	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:49752889-49762689	GM12892	blood:	n/a	n/a
36	POLR2A	chr3:49755867-49757493	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr3:49755494-49757480	MCF-7	breast:	n/a	n/a
38	BCL3	chr3:49756106-49756302	K562	blood:	n/a	n/a
39	ZNF143	chr3:49756053-49756225	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:49752911-49757637	HL-60	blood:	n/a	n/a
41	POLR2A	chr3:49755479-49757470	GM19193	blood:	n/a	n/a
42	PBX3	chr3:49755730-49759087	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr3:49752081-49757341	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:49756136-49757123	HepG2	liver:	n/a	n/a
45	ELF1	chr3:49755770-49756267	GM12878	blood:	n/a	n/a
46	GABPA	chr3:49755803-49757175	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3A	chr3:49756075-49757347	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:49754271-49762558	U87	brain:	n/a	n/a
49	E2F6	chr3:49755534-49757519	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:49755297-49756649	PFSK-1	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:48784693..48785277-chr3:49756207..49757193,2	Hela-S3	cervix:
2	chr3:49724349..49727675-chr3:49755739..49757510,3	MCF-7	breast:

No data

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000154945	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173531	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs34127462	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1796605	chr3:49744556-49760567	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv482082	chr3:49754965-49757123	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:49736800-49756400	Weak transcription	HSMM	muscle
3	chr3:49739000-49756400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:49740200-49756600	Weak transcription	HSMMtube	muscle
5	chr3:49740600-49759800	Weak transcription	Hela-S3	cervix
6	chr3:49740800-49756400	Weak transcription	Osteobl	bone
7	chr3:49743000-49756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:49743000-49756800	Weak transcription	Small Intestine	intestine
9	chr3:49744000-49756400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:49746400-49756600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49749400-49756600	Weak transcription	A549	lung
12	chr3:49749800-49756400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr3:49751400-49756400	Strong transcription	NHLF	lung
14	chr3:49752600-49759800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:49753000-49759600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:49753400-49757400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:49753600-49758200	Weak transcription	HepG2	liver
18	chr3:49753600-49759400	Weak transcription	K562	blood
19	chr3:49753800-49756400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49753800-49756800	Weak transcription	Aorta	Aorta
21	chr3:49755000-49756400	Bivalent Enhancer	Fetal Stomach	stomach
22	chr3:49755000-49756400	Strong transcription	Dnd41	blood
23	chr3:49755000-49757600	Enhancers	Fetal Heart	heart
24	chr3:49755400-49756400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:49755400-49756400	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:49755400-49756400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:49755400-49756400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:49755400-49756400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr3:49755400-49756400	Enhancers	Pancreas	Pancrea
30	chr3:49755400-49756600	Enhancers	HMEC	breast
31	chr3:49755600-49756400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:49755600-49756400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:49755600-49756400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:49755600-49756600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:49755600-49756600	Enhancers	Fetal Brain Male	brain
36	chr3:49755600-49756600	Enhancers	Placenta	Placenta
37	chr3:49755600-49756600	Enhancers	Lung	lung
38	chr3:49755600-49756600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:49755600-49757400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:49755800-49756400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr3:49755800-49756400	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:49755800-49756400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:49755800-49756400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:49755800-49756400	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr3:49755800-49756400	Enhancers	Right Ventricle	heart
46	chr3:49755800-49756400	Bivalent Enhancer	HUVEC	blood vessel
47	chr3:49755800-49756600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:49755800-49756600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:49755800-49756600	Enhancers	Right Atrium	heart
50	chr3:49755800-49756600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle

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