Variant report

Variant	rs17099879
Chromosome Location	chr12:64257969-64257970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64257945..64259859-chr12:64259892..64262492,3	MCF-7	breast:
2	chr12:64257643..64259888-chr12:64403526..64405520,2	MCF-7	breast:
3	chr12:64254678..64258025-chr12:64259314..64262432,3	MCF-7	breast:
4	chr12:64248653..64250464-chr12:64256025..64258029,2	MCF-7	breast:
5	chr12:64257915..64259746-chr12:64264033..64266487,2	K562	blood:

Variant related genes	Relation type
ENSG00000242087	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11837218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17099872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17099873	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17099886	0.95[CHD][hapmap];0.92[TSI][hapmap]
rs17099889	0.95[CHD][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs17099893	0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs4346062	0.95[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
5	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
6	esv1803717	chr12:64250221-64261249	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17099879	TMEM5	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:64241000-64268800	Weak transcription	Lung	lung
3	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
4	chr12:64243400-64263000	Weak transcription	NHEK	skin
5	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
6	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
7	chr12:64247800-64268200	Weak transcription	Fetal Brain Male	brain
8	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
9	chr12:64254200-64259200	Enhancers	Fetal Intestine Large	intestine
10	chr12:64255000-64258600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:64255200-64258000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:64255200-64258600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:64255200-64259000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:64255400-64258600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:64255800-64258400	Enhancers	Osteobl	bone
16	chr12:64256200-64258000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:64256200-64258400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:64256400-64258000	Weak transcription	Fetal Kidney	kidney
19	chr12:64256400-64258200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:64256400-64258400	Weak transcription	Adipose Nuclei	Adipose
21	chr12:64256400-64258400	Flanking Active TSS	A549	lung
22	chr12:64256600-64262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:64256600-64263600	Weak transcription	HSMMtube	muscle
24	chr12:64256800-64258600	Enhancers	Hela-S3	cervix
25	chr12:64256800-64258800	Enhancers	Fetal Intestine Small	intestine
26	chr12:64256800-64259200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:64256800-64260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:64256800-64260600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:64256800-64262200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:64256800-64263200	Weak transcription	Right Atrium	heart
31	chr12:64256800-64271400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:64256800-64276600	Weak transcription	HSMM	muscle
33	chr12:64256800-64282600	Weak transcription	Gastric	stomach
34	chr12:64257000-64258000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:64257000-64258000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:64257000-64258400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:64257000-64258400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:64257000-64258400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:64257000-64259400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:64257000-64259400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:64257000-64259400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:64257000-64262600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:64257000-64262800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:64257000-64263600	Weak transcription	NH-A	brain
45	chr12:64257200-64258600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr12:64257200-64259400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:64257200-64259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:64257400-64262000	Weak transcription	Left Ventricle	heart
49	chr12:64257400-64263200	Weak transcription	NHDF-Ad	bronchial
50	chr12:64257400-64270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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