Variant report

Variant	rs3766930
Chromosome Location	chr1:225653427-225653428
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	chr1:225652612-225653522	Hela-S3	cervix:	n/a	n/a
2	USF2	chr1:225653044-225653459	Hela-S3	cervix:	n/a	n/a
3	MYC	chr1:225653121-225653433	MCF10A-Er-Src	breast:	n/a	n/a
4	CHD2	chr1:225652644-225653524	Hela-S3	cervix:	n/a	n/a
5	RFX5	chr1:225652584-225653530	Hela-S3	cervix:	n/a	n/a
6	MAFK	chr1:225652660-225653474	Hela-S3	cervix:	n/a	n/a
7	ZNF143	chr1:225652588-225653509	Hela-S3	cervix:	n/a	chr1:225653269-225653288
8	TFAP2A	chr1:225652680-225653795	Hela-S3	cervix:	n/a	chr1:225653222-225653232 chr1:225653222-225653232 chr1:225653220-225653234 chr1:225653222-225653232 chr1:225653220-225653235
9	SMARCC1	chr1:225652648-225653667	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:225652654-225653483	Hela-S3	cervix:	n/a	n/a
11	TBP	chr1:225652832-225653443	Hela-S3	cervix:	n/a	n/a
12	MYC	chr1:225652605-225653483	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:225652751-225653453	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr1:225652646-225653513	Hela-S3	cervix:	n/a	n/a
15	EP300	chr1:225653000-225653433	Hela-S3	cervix:	n/a	n/a
16	TFAP2C	chr1:225652593-225653834	Hela-S3	cervix:	n/a	chr1:225653220-225653235 chr1:225653054-225653063
17	MAX	chr1:225652675-225653525	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr1:225652781-225653495	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:225652314-225653840	Hela-S3	cervix:	n/a	n/a
20	MYC	chr1:225653088-225653467	MCF10A-Er-Src	breast:	n/a	n/a
21	BRCA1	chr1:225653015-225653483	Hela-S3	cervix:	n/a	n/a
22	ZNF263	chr1:225652611-225653640	HEK293-T-REx	kidney:	n/a	n/a
23	TCF12	chr1:225652870-225653522	ECC-1	luminal epithelium:	n/a	n/a
24	MAZ	chr1:225652763-225653537	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:225652725-225653556	Hela-S3	cervix:	n/a	n/a
26	SMC3	chr1:225652648-225653576	Hela-S3	cervix:	n/a	n/a
27	MAX	chr1:225652751-225653478	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr1:225653033-225653474	Hela-S3	cervix:	n/a	n/a
29	RCOR1	chr1:225652743-225653575	Hela-S3	cervix:	n/a	n/a
30	TCF7L2	chr1:225652689-225653562	Hela-S3	cervix:	n/a	n/a
31	GTF2F1	chr1:225652780-225653461	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225652849..225654996-chr1:225964946..225967311,2	MCF-7	breast:
2	chr1:91487179..91487687-chr1:225653229..225653962,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000234476	TF binding region
ENSG00000122482	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10799312	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915831	0.80[ASN][1000 genomes]
rs11588279	0.92[CHB][hapmap]
rs12032961	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12034829	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs12124353	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12742313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1340865	1.00[CHB][hapmap]
rs1340867	0.82[CHB][hapmap]
rs1891000	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs2066233	0.92[CHB][hapmap]
rs2185528	0.80[ASN][1000 genomes]
rs3856157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3893032	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4233220	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4554690	0.92[AFR][1000 genomes]
rs499782	1.00[CHB][hapmap]
rs6426075	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs6692054	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6696038	0.92[CHB][hapmap]
rs7536925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552953	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv34905	chr1:225631404-225676582	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225642400-225655200	Weak transcription	Small Intestine	intestine
2	chr1:225642600-225655000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:225646400-225653600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225647000-225653600	Enhancers	Esophagus	oesophagus
5	chr1:225647000-225654600	Enhancers	Fetal Thymus	thymus
6	chr1:225647000-225654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:225647400-225654800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:225647600-225653800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:225648800-225654600	Weak transcription	HUVEC	blood vessel
10	chr1:225649000-225654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:225649200-225654400	Weak transcription	Primary T cells from cord blood	blood
12	chr1:225649800-225654800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:225649800-225662600	Weak transcription	Pancreas	Pancrea
14	chr1:225650000-225653600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:225650200-225653800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:225650200-225654600	Weak transcription	Spleen	Spleen
17	chr1:225650600-225653600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:225650800-225653600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:225650800-225653600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:225650800-225653800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:225651000-225653600	Enhancers	HMEC	breast
22	chr1:225651200-225655200	Weak transcription	Right Ventricle	heart
23	chr1:225651400-225653600	Weak transcription	Thymus	Thymus
24	chr1:225651400-225654600	Weak transcription	Lung	lung
25	chr1:225651400-225662400	Weak transcription	Fetal Brain Male	brain
26	chr1:225651600-225654400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:225651600-225655000	Weak transcription	Stomach Mucosa	stomach
28	chr1:225651600-225655200	Weak transcription	Fetal Intestine Small	intestine
29	chr1:225651800-225653800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:225651800-225654800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:225652000-225653600	Enhancers	Fetal Muscle Leg	muscle
32	chr1:225652000-225653600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:225652000-225653800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:225652000-225654400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:225652000-225655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:225652200-225653800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:225652200-225654000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:225652400-225653600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr1:225652400-225653600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:225652400-225653600	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:225652400-225653600	Enhancers	NH-A	brain
42	chr1:225652400-225654000	Enhancers	Fetal Stomach	stomach
43	chr1:225652400-225655000	Enhancers	Rectal Smooth Muscle	rectum
44	chr1:225652400-225655200	Weak transcription	NHLF	lung
45	chr1:225652600-225653600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:225652600-225653600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:225652600-225653600	Flanking Active TSS	HepG2	liver
48	chr1:225652600-225653800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:225652600-225653800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:225652600-225654000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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