Variant report

Variant	rs10861399
Chromosome Location	chr12:105730275-105730276
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	chr12:105628021..105630375-chr12:105728752..105731859,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10861401	0.86[YRI][hapmap]
rs10861402	0.87[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs11112474	0.91[LWK][hapmap];0.86[YRI][hapmap]
rs12228619	0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs2060204	0.80[YRI][hapmap]
rs34483838	0.80[ASN][1000 genomes]
rs715167	0.86[YRI][hapmap]
rs7300844	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7302174	0.81[MEX][hapmap]
rs8181654	0.93[ASN][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	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10861399	C12orf75	cis	Artery Aorta	GTEx
rs10861399	BTBD11	cis	cerebellum	SCAN
rs10861399	C12orf75	cis	Artery Tibial	GTEx
rs10861399	APPL2	cis	lymphoblastoid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105725200-105734600	Weak transcription	Esophagus	oesophagus
2	chr12:105725600-105747200	Weak transcription	Gastric	stomach
3	chr12:105725800-105734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:105726000-105731200	Weak transcription	Hela-S3	cervix
5	chr12:105726000-105734600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:105726000-105734600	Weak transcription	Fetal Intestine Small	intestine
7	chr12:105726200-105731200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:105726200-105731200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:105726200-105731200	Weak transcription	HepG2	liver
10	chr12:105726200-105734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:105727000-105731000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:105727000-105734600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:105727200-105734400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:105727400-105734400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:105727800-105730600	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:105727800-105737200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:105728000-105736000	Weak transcription	HUVEC	blood vessel
18	chr12:105728400-105734600	Weak transcription	HSMMtube	muscle
19	chr12:105728600-105734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:105728600-105734600	Weak transcription	Fetal Stomach	stomach
21	chr12:105728800-105730400	Weak transcription	HSMM	muscle
22	chr12:105728800-105734400	Weak transcription	HMEC	breast
23	chr12:105729000-105732000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:105729000-105732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:105729000-105733800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:105729000-105734400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:105729000-105734400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:105729200-105730600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:105729200-105730600	Genic enhancers	NHDF-Ad	bronchial
30	chr12:105729200-105731800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:105729400-105731600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:105729400-105734400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:105729600-105730400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:105729600-105731200	Weak transcription	Osteobl	bone
35	chr12:105729600-105731600	Genic enhancers	Dnd41	blood
36	chr12:105729600-105732200	Enhancers	Fetal Thymus	thymus
37	chr12:105729800-105730400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:105729800-105730600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:105729800-105730600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:105729800-105731200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:105729800-105731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:105729800-105731200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:105729800-105731200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:105729800-105731400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:105729800-105731400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:105729800-105731800	Genic enhancers	A549	lung
47	chr12:105729800-105732600	Enhancers	Placenta	Placenta
48	chr12:105729800-105734400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:105729800-105736200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:105729800-105736800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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