Variant report

Variant	rs17823442
Chromosome Location	chr12:65056935-65056936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65018082..65020499-chr12:65056309..65058062,2	MCF-7	breast:
2	chr12:65056922..65058477-chr12:65065654..65067212,2	MCF-7	breast:
3	chr12:65052809..65057166-chr12:65058772..65061911,4	MCF-7	breast:
4	chr12:65056764..65058467-chr12:65059357..65061910,2	K562	blood:
5	chr12:65048771..65052782-chr12:65056802..65060601,5	MCF-7	breast:
6	chr12:65003105..65006170-chr12:65055260..65058498,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153179	Chromatin interaction
ENSG00000256670	Chromatin interaction
ENSG00000256314	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1008159	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1008160	0.83[EUR][1000 genomes]
rs11175471	0.85[CEU][hapmap]
rs11175476	0.85[CEU][hapmap]
rs11175478	0.85[CEU][hapmap]
rs11175497	0.82[AMR][1000 genomes]
rs11175509	0.86[EUR][1000 genomes]
rs11837759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12230536	0.85[CEU][hapmap]
rs12814316	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12816847	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12824246	0.82[AMR][1000 genomes]
rs12829878	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830436	0.85[CEU][hapmap]
rs12831875	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12833931	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223244	0.85[CEU][hapmap]
rs17223377	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17223391	0.87[EUR][1000 genomes]
rs2078398	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs35674528	0.87[EUR][1000 genomes]
rs7303641	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7304648	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7959471	0.82[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
2	chr12:65033600-65059400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr12:65043600-65059600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:65044000-65059400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:65046400-65058600	Weak transcription	Ovary	ovary
6	chr12:65047000-65059400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:65047200-65059400	Weak transcription	Fetal Stomach	stomach
8	chr12:65047400-65059400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr12:65047800-65059400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:65047800-65059400	Weak transcription	NHLF	lung
11	chr12:65047800-65063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:65048000-65060400	Weak transcription	Dnd41	blood
13	chr12:65048000-65063000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:65048400-65062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:65048600-65059400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:65048800-65060200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:65049000-65059600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:65049200-65058800	Weak transcription	K562	blood
19	chr12:65049200-65062200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:65049400-65059000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:65049800-65059600	Weak transcription	Placenta	Placenta
22	chr12:65050400-65059400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:65050400-65059400	Weak transcription	NH-A	brain
24	chr12:65050600-65058800	Weak transcription	Liver	Liver
25	chr12:65051400-65057000	Enhancers	Fetal Heart	heart
26	chr12:65051600-65060600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:65052200-65057200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:65052800-65059200	Weak transcription	Lung	lung
29	chr12:65052800-65059400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:65053000-65057200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr12:65053000-65058400	Weak transcription	Primary B cells from cord blood	blood
32	chr12:65053000-65058800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:65053000-65059400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:65053000-65059400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr12:65053000-65059600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:65053200-65058200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:65053200-65058800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:65053400-65057800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:65053400-65058400	Weak transcription	Small Intestine	intestine
40	chr12:65053400-65058600	Weak transcription	HUVEC	blood vessel
41	chr12:65053400-65058800	Weak transcription	Fetal Kidney	kidney
42	chr12:65053400-65058800	Weak transcription	Right Atrium	heart
43	chr12:65053400-65059200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:65053400-65059200	Weak transcription	Fetal Intestine Small	intestine
45	chr12:65053400-65059400	Weak transcription	Adipose Nuclei	Adipose
46	chr12:65053400-65059400	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:65053600-65059200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:65054800-65058600	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:65054800-65059400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:65054800-65060400	Weak transcription	Aorta	Aorta

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