Variant report

Variant	rs3754582
Chromosome Location	chr2:187349979-187349980
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	MXI1	chr2:187349908-187352518	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:187349863-187352422	MCF10A-Er-Src	breast:	n/a	n/a
3	MBD4	chr2:187349546-187351735	HepG2	liver:	n/a	n/a
4	MYC	chr2:187349894-187351872	A549	lung:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
5	POLR2A	chr2:187349964-187350176	ProgFib	skin:	n/a	n/a
6	HEY1	chr2:187349947-187351663	HepG2	liver:	n/a	n/a
7	CREB1	chr2:187349971-187352009	K562	blood:	n/a	n/a
8	MBD4	chr2:187349952-187351605	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:187349962-187351739	Hela-S3	cervix:	n/a	n/a
10	CHD1	chr2:187348914-187351966	GM12878	blood:	n/a	n/a
11	IRF1	chr2:187349709-187351482	K562	blood:	n/a	chr2:187350311-187350322 chr2:187350534-187350548 chr2:187350710-187350727 chr2:187350708-187350722 chr2:187350709-187350722
12	MYBL2	chr2:187349882-187352186	HepG2	liver:	n/a	n/a
13	IRF1	chr2:187349040-187352404	K562	blood:	n/a	chr2:187350311-187350322 chr2:187349270-187349282 chr2:187349271-187349282 chr2:187350534-187350548 chr2:187349269-187349282 chr2:187349271-187349285 chr2:187350710-187350727 chr2:187350708-187350722 chr2:187349270-187349284 chr2:187350709-187350722 chr2:187349270-187349283 chr2:187351805-187351819 chr2:187349267-187349281
14	POLR2A	chr2:187348798-187352419	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:187348502-187352426	GM12891	blood:	n/a	n/a
16	POLR2A	chr2:187349913-187352210	GM12878	blood:	n/a	n/a
17	GATA1	chr2:187349622-187351879	PBDE	blood:	n/a	chr2:187350409-187350418 chr2:187350409-187350416 chr2:187349842-187349851 chr2:187350408-187350418 chr2:187349882-187349903
18	POLR2A	chr2:187349541-187352452	GM12878	blood:	n/a	n/a
19	MXI1	chr2:187349490-187352240	IMR90	lung:	n/a	n/a
20	TEAD4	chr2:187348424-187351525	HepG2	liver:	n/a	chr2:187349483-187349492
21	MYC	chr2:187349900-187352155	MCF10A-Er-Src	breast:	n/a	chr2:187351278-187351289 chr2:187351281-187351288 chr2:187351274-187351293 chr2:187351278-187351289 chr2:187351280-187351289 chr2:187351279-187351288 chr2:187351277-187351290 chr2:187351277-187351290 chr2:187351279-187351289 chr2:187351278-187351289 chr2:187351279-187351289
22	MAFK	chr2:187349976-187351208	K562	blood:	n/a	n/a
23	MYBL2	chr2:187349927-187351653	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:187349968-187351991	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:187349746-187352018	GM18505	blood:	n/a	n/a
26	POLR2A	chr2:187349962-187352507	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:187349481-187352594	IMR90	lung:	n/a	n/a
28	CHD1	chr2:187349426-187352572	IMR90	lung:	n/a	n/a
29	POLR2A	chr2:187349970-187351800	SK-N-MC	brain:	n/a	n/a
30	TRIM28	chr2:187349921-187351880	K562	blood:	n/a	n/a
31	ARID3A	chr2:187349651-187351560	HepG2	liver:	n/a	chr2:187350480-187350496

No.	Distal block	Cell Line	Cell type
1	chr2:187331928..187334444-chr2:187348052..187350692,2	MCF-7	breast:
2	chr2:187349672..187352615-chr2:187454696..187458504,4	K562	blood:
3	chr2:187348777..187350496-chr2:187367699..187370297,2	MCF-7	breast:
4	chr2:187347068..187348940-chr2:187349193..187350808,2	MCF-7	breast:

Variant related genes	Relation type
ZC3H15	TF binding region
ENSG00000065548	Chromatin interaction
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1026118	0.86[JPT][hapmap]
rs10931241	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622084	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12993773	0.82[JPT][hapmap]
rs1376781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597244	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16827774	0.80[ASN][1000 genomes]
rs16827790	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16827800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2029085	0.81[ASN][1000 genomes]
rs4144823	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4606885	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667100	0.81[JPT][hapmap]
rs57550664	0.81[ASN][1000 genomes]
rs59228985	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61538288	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62198657	0.84[ASN][1000 genomes]
rs72893443	0.81[ASN][1000 genomes]
rs72893458	0.81[ASN][1000 genomes]
rs72893482	0.80[ASN][1000 genomes]
rs72895425	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72895447	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72895498	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72897378	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561955	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9636305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187328000-187350400	Weak transcription	Pancreas	Pancrea
2	chr2:187346600-187350000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:187348200-187350000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr2:187348200-187350000	Active TSS	Duodenum Mucosa	Duodenum
5	chr2:187348200-187352200	Active TSS	Colonic Mucosa	Colon
6	chr2:187348200-187353400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr2:187348400-187350400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:187348600-187350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:187348600-187350000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:187348600-187350000	Weak transcription	Ovary	ovary
11	chr2:187348600-187352600	Active TSS	Fetal Intestine Small	intestine
12	chr2:187348600-187353000	Active TSS	Fetal Intestine Large	intestine
13	chr2:187348800-187350000	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:187348800-187350000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:187348800-187350000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:187348800-187350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:187348800-187350200	Enhancers	Stomach Mucosa	stomach
18	chr2:187348800-187350400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr2:187348800-187350400	Flanking Active TSS	Dnd41	blood
20	chr2:187348800-187350600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:187348800-187352200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr2:187348800-187353200	Active TSS	K562	blood
23	chr2:187349000-187350000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:187349000-187350000	Enhancers	Liver	Liver
25	chr2:187349000-187350000	Enhancers	Brain Angular Gyrus	brain
26	chr2:187349000-187350000	Enhancers	Brain Substantia Nigra	brain
27	chr2:187349000-187350000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr2:187349000-187350000	Enhancers	Hela-S3	cervix
29	chr2:187349000-187350000	Enhancers	Osteobl	bone
30	chr2:187349000-187350400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:187349000-187350600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:187349000-187352800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:187349000-187353200	Active TSS	GM12878-XiMat	blood
34	chr2:187349000-187354000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr2:187349200-187350000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:187349200-187350000	Enhancers	Thymus	Thymus
37	chr2:187349200-187351000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:187349200-187352200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:187349400-187350000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:187349400-187350000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:187349400-187350000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr2:187349400-187350000	Enhancers	Brain Anterior Caudate	brain
43	chr2:187349400-187350000	Enhancers	Brain Hippocampus Middle	brain
44	chr2:187349400-187350000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:187349400-187350000	Enhancers	Fetal Lung	lung
46	chr2:187349400-187350000	Enhancers	Fetal Muscle Leg	muscle
47	chr2:187349400-187350000	Enhancers	Fetal Thymus	thymus
48	chr2:187349400-187350000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr2:187349400-187350200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:187349400-187350400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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