Variant report

Variant	rs7297499
Chromosome Location	chr12:49099850-49099851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49099371..49102358-chr12:49106962..49108782,2	MCF-7	breast:
2	chr12:49074433..49077876-chr12:49098610..49102767,4	MCF-7	breast:
3	chr12:49098999..49101688-chr12:49103437..49107228,4	MCF-7	breast:
4	chr12:49074052..49077254-chr12:49096800..49101145,7	MCF-7	breast:
5	chr12:49075555..49077522-chr12:49096426..49100046,3	K562	blood:

Variant related genes	Relation type
ENSG00000139620	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11830884	1.00[AFR][1000 genomes]
rs11837122	0.93[AFR][1000 genomes]
rs11838009	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11838289	0.90[AFR][1000 genomes]
rs11838360	1.00[AFR][1000 genomes]
rs2453489	1.00[CEU][hapmap]
rs2898086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs34046666	0.83[AMR][1000 genomes]
rs35678179	0.96[EUR][1000 genomes]
rs57337154	1.00[AFR][1000 genomes]
rs57454425	1.00[AFR][1000 genomes]
rs60351852	1.00[AFR][1000 genomes]
rs61496293	0.83[AMR][1000 genomes]
rs61751603	0.96[EUR][1000 genomes]
rs7299151	0.83[AMR][1000 genomes]
rs7312311	1.00[AFR][1000 genomes]
rs7315319	1.00[ASW][hapmap];0.87[YRI][hapmap]
rs74088105	0.90[AFR][1000 genomes]
rs74088110	0.90[AFR][1000 genomes]
rs74088131	0.83[AFR][1000 genomes]
rs74088137	1.00[AFR][1000 genomes]
rs74088149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74088163	0.93[AFR][1000 genomes]
rs74088167	0.93[AFR][1000 genomes]

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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 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	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49081000-49101000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:49081400-49104000	Strong transcription	Hela-S3	cervix
4	chr12:49081600-49103800	Strong transcription	Dnd41	blood
5	chr12:49081600-49107200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:49081600-49107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:49081600-49108400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:49082000-49104000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:49082000-49107600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:49082200-49100800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:49082200-49107200	Strong transcription	Liver	Liver
12	chr12:49082200-49107400	Strong transcription	Placenta	Placenta
13	chr12:49082200-49108000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:49082200-49108400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:49082200-49108600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:49082200-49108600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:49082200-49108800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:49082400-49100200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:49082600-49107600	Strong transcription	Fetal Thymus	thymus
20	chr12:49082800-49101800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:49088200-49107200	Weak transcription	Small Intestine	intestine
22	chr12:49088200-49107400	Weak transcription	Psoas Muscle	Psoas
23	chr12:49088200-49107600	Weak transcription	Stomach Mucosa	stomach
24	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:49090000-49107200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:49090000-49107600	Weak transcription	Brain Angular Gyrus	brain
27	chr12:49090000-49107800	Weak transcription	Fetal Heart	heart
28	chr12:49090000-49108400	Weak transcription	Fetal Brain Male	brain
29	chr12:49091800-49103400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:49091800-49104800	Strong transcription	GM12878-XiMat	blood
31	chr12:49091800-49107400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:49092800-49100800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:49093400-49102800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:49093400-49108000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr12:49095000-49108600	Strong transcription	Fetal Stomach	stomach
36	chr12:49095200-49103400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:49095400-49100200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:49095600-49102200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:49095600-49102800	Strong transcription	Thymus	Thymus
40	chr12:49095600-49103000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:49095600-49107400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:49095600-49107800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:49095600-49108800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:49095800-49100000	Strong transcription	Fetal Intestine Large	intestine
45	chr12:49095800-49100000	Strong transcription	Fetal Muscle Leg	muscle
46	chr12:49095800-49100200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:49095800-49100200	Strong transcription	NH-A	brain
48	chr12:49095800-49101800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:49095800-49103200	Strong transcription	Osteobl	bone
50	chr12:49095800-49107200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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