Variant report

Variant	rs11540500
Chromosome Location	chr3:49051028-49051029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49050562-49051861	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:49049755-49051806	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:49050020-49052092	HL-60	blood:	n/a	n/a
4	POLR2A	chr3:49049292-49051808	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49049236-49052057	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr3:49049681-49055610	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:49048502-49056486	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49048842-49056486	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:49048845-49056419	GM12891	blood:	n/a	n/a
11	POLR2A	chr3:49050482-49051314	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:49050742-49051780	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49050102-49051333	A549	lung:	n/a	n/a
14	POLR2A	chr3:49049436-49051302	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:49050908-49056374	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr3:49048918-49055399	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:49050847-49051256	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:49048918-49052189	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:49048783-49056505	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:49049988-49051938	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:49050657-49051358	GM12891	blood:	n/a	n/a
22	POLR2A	chr3:49049496-49052939	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:49048897-49056290	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:49050714-49051118	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:49050527-49051946	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:49049843-49052968	HL-60	blood:	n/a	n/a
27	POLR2A	chr3:49050568-49056569	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr3:49048769-49067292	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:49050528-49052929	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr3:49050154-49067307	K562	blood:	n/a	n/a
31	POLR2A	chr3:49050107-49051134	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:49050623-49059964	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr3:49049321-49056950	K562	blood:	n/a	n/a
34	POLR2A	chr3:49049735-49052929	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49049216..49051915-chr3:49137148..49139973,2	MCF-7	breast:
2	chr3:49050440..49054790-chr3:49130798..49133846,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR6	TF binding region
ENSG00000198218	Chromatin interaction
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11713750	1.00[MEX][hapmap]
rs13089613	1.00[MEX][hapmap]
rs28673107	1.00[CHD][hapmap]
rs35806761	1.00[LWK][hapmap];1.00[MEX][hapmap]
rs35989076	1.00[CHD][hapmap]
rs9857248	1.00[MEX][hapmap]
rs9865051	1.00[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 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	chr3:49045600-49052200	Weak transcription	Small Intestine	intestine
2	chr3:49045800-49055000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49046000-49052000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:49046200-49051400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:49046200-49051400	Weak transcription	HUVEC	blood vessel
6	chr3:49046200-49052000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:49046200-49052000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:49046200-49052000	Weak transcription	Fetal Kidney	kidney
9	chr3:49046200-49054400	Strong transcription	Fetal Stomach	stomach
10	chr3:49046200-49054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:49046200-49054600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:49046200-49054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:49046400-49052400	Weak transcription	Fetal Brain Male	brain
14	chr3:49046400-49054200	Strong transcription	Fetal Intestine Small	intestine
15	chr3:49046600-49054200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:49046800-49054200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49046800-49054400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:49047000-49052400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:49047000-49054200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49047200-49051200	Weak transcription	Hela-S3	cervix
21	chr3:49047600-49054800	Strong transcription	Lung	lung
22	chr3:49048400-49051200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:49048400-49054400	Strong transcription	Fetal Intestine Large	intestine
24	chr3:49048400-49054600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:49048600-49053400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:49048600-49054400	Strong transcription	Thymus	Thymus
27	chr3:49048800-49051800	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr3:49048800-49051800	Genic enhancers	Fetal Muscle Leg	muscle
29	chr3:49048800-49051800	Genic enhancers	Pancreas	Pancrea
30	chr3:49048800-49052800	Genic enhancers	Spleen	Spleen
31	chr3:49048800-49053800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:49048800-49053800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:49048800-49053800	Strong transcription	Fetal Thymus	thymus
34	chr3:49048800-49054000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:49048800-49054000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:49048800-49054000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:49048800-49054000	Strong transcription	Primary B cells from cord blood	blood
38	chr3:49048800-49054000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:49048800-49054200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:49048800-49054200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:49048800-49054200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:49048800-49054200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:49048800-49054200	Strong transcription	Primary T cells from cord blood	blood
44	chr3:49048800-49054200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:49048800-49054200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:49048800-49054400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:49048800-49054400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:49048800-49054400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:49048800-49054400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:49048800-49054600	Strong transcription	Fetal Brain Female	brain

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