Variant report

Variant	rs2629755
Chromosome Location	chr12:104492003-104492004
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	chr12:104486963..104489819-chr12:104491928..104495052,4	K562	blood:
2	chr12:104490343..104492832-chr12:104530682..104533569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10861159	0.90[ASN][1000 genomes]
rs10861160	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11111921	0.85[MEX][hapmap]
rs2466551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2466554	0.84[EUR][1000 genomes]
rs2629745	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2629754	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700499	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2930856	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964534	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6539125	0.93[MEX][hapmap]
rs715664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7306771	0.86[JPT][hapmap]
rs7309185	0.90[JPT][hapmap]
rs7315351	0.84[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	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2629755	CHST11	cis	cerebellum	SCAN
rs2629755	PMCH	cis	cerebellum	SCAN
rs2629755	EID3	cis	brain	BrainEAC

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104460000-104496800	Weak transcription	HepG2	liver
2	chr12:104460000-104511800	Weak transcription	Hela-S3	cervix
3	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
4	chr12:104461200-104492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:104471000-104499600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:104471400-104500000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:104472000-104497400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:104472400-104497400	Strong transcription	Placenta	Placenta
9	chr12:104472400-104501200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:104472600-104497200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:104476200-104497400	Strong transcription	Adipose Nuclei	Adipose
12	chr12:104477200-104508400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:104478200-104492800	Weak transcription	NHEK	skin
14	chr12:104478400-104492800	Weak transcription	Spleen	Spleen
15	chr12:104478600-104499400	Weak transcription	Fetal Heart	heart
16	chr12:104480000-104508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:104480600-104497600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:104481000-104495000	Weak transcription	Esophagus	oesophagus
19	chr12:104481000-104499400	Weak transcription	Stomach Mucosa	stomach
20	chr12:104481000-104500800	Weak transcription	K562	blood
21	chr12:104481200-104492400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:104482400-104493000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:104482600-104492800	Weak transcription	Fetal Brain Male	brain
24	chr12:104482800-104492400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:104482800-104508200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:104483200-104492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:104483200-104492800	Weak transcription	Gastric	stomach
28	chr12:104483200-104492800	Weak transcription	Pancreas	Pancrea
29	chr12:104483400-104492400	Weak transcription	Fetal Intestine Small	intestine
30	chr12:104483400-104492800	Weak transcription	A549	lung
31	chr12:104483800-104492800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:104483800-104493000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:104485000-104500800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:104485200-104493000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:104485200-104495600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr12:104486200-104492400	Weak transcription	Fetal Stomach	stomach
37	chr12:104486200-104503000	Weak transcription	Small Intestine	intestine
38	chr12:104486800-104495800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:104487000-104497200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:104487000-104497800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:104487200-104492600	Strong transcription	Fetal Thymus	thymus
42	chr12:104487200-104493400	Strong transcription	Dnd41	blood
43	chr12:104487200-104494000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:104487200-104495600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:104487200-104496000	Strong transcription	HSMMtube	muscle
46	chr12:104487200-104497000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:104487200-104497200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:104487200-104497200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:104487200-104497400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:104487200-104497600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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