Variant report

Variant	rs10492349
Chromosome Location	chr12:10790828-10790829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10782352..10785232-chr12:10787939..10791326,3	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16922916	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs2125088	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2417908	0.94[CEU][hapmap]
rs897881	0.94[CEU][hapmap];0.80[EUR][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	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv607	chr12:10776867-10821535	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10492349	STYK1	cis	parietal	SCAN
rs10492349	KLRC2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10794400	Weak transcription	Gastric	stomach
2	chr12:10782200-10791000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:10785400-10792600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:10787000-10793800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:10787600-10794000	Weak transcription	NHEK	skin
6	chr12:10787600-10794200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:10787600-10794200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:10787800-10792800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:10787800-10794000	Weak transcription	HMEC	breast
10	chr12:10787800-10797800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:10788000-10792400	Weak transcription	Osteobl	bone
12	chr12:10788000-10794000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:10788000-10794400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:10788400-10791000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:10788600-10797400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:10788800-10792600	Weak transcription	NHDF-Ad	bronchial
17	chr12:10788800-10793400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:10789800-10793800	Weak transcription	Placenta	Placenta
19	chr12:10789800-10794000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:10789800-10794000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:10789800-10794000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:10789800-10795000	Enhancers	Stomach Mucosa	stomach
23	chr12:10790000-10791000	Weak transcription	HUVEC	blood vessel
24	chr12:10790400-10791800	Enhancers	Duodenum Mucosa	Duodenum
25	chr12:10790600-10799200	Weak transcription	Esophagus	oesophagus
26	chr12:10790800-10791400	Active TSS	Rectal Mucosa Donor 29	rectum

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