Variant report

Variant	rs12522269
Chromosome Location	chr5:70938092-70938093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70937966..70939706-chr5:70940966..70942918,2	MCF-7	breast:
2	chr5:70891609..70893617-chr5:70937357..70939064,2	MCF-7	breast:
3	chr5:70930390..70934601-chr5:70935196..70939070,4	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

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

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

rs_ID	r²[population]
rs10071645	0.81[EUR][1000 genomes]
rs10073617	0.83[EUR][1000 genomes]
rs1391179	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553314	0.83[EUR][1000 genomes]
rs2270920	0.83[EUR][1000 genomes]
rs7379017	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7379830	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7380859	0.80[ASN][1000 genomes]
rs7443786	0.88[ASN][1000 genomes]
rs7444180	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12522269	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
2	chr5:70898200-70944200	Weak transcription	Osteobl	bone
3	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
5	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
8	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:70912600-70943800	Weak transcription	A549	lung
11	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:70915400-70950800	Weak transcription	NHLF	lung
13	chr5:70917000-70945000	Weak transcription	Hela-S3	cervix
14	chr5:70917200-70942000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:70917400-70942600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:70918000-70942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:70919800-70955000	Weak transcription	HUVEC	blood vessel
18	chr5:70925400-70950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:70926600-70954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:70927000-70939600	Strong transcription	Fetal Intestine Large	intestine
21	chr5:70927000-70939800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:70927000-70954000	Strong transcription	Dnd41	blood
23	chr5:70927000-70954200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:70927200-70940200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:70927400-70938200	Weak transcription	Spleen	Spleen
26	chr5:70927600-70940000	Strong transcription	Liver	Liver
27	chr5:70927600-70940200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr5:70928000-70940200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:70928000-70940200	Strong transcription	Adipose Nuclei	Adipose
30	chr5:70928000-70940200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:70928600-70943800	Weak transcription	Thymus	Thymus
32	chr5:70928800-70942800	Weak transcription	Fetal Thymus	thymus
33	chr5:70928800-70945800	Weak transcription	NHEK	skin
34	chr5:70929600-70940000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:70930000-70939800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:70930200-70938800	Strong transcription	Left Ventricle	heart
37	chr5:70930200-70940400	Strong transcription	Primary B cells from cord blood	blood
38	chr5:70930400-70938200	Weak transcription	Esophagus	oesophagus
39	chr5:70930400-70938800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:70930400-70952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:70930600-70938400	Weak transcription	HSMMtube	muscle
42	chr5:70930600-70941600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr5:70931400-70938200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:70931400-70942200	Weak transcription	Psoas Muscle	Psoas
45	chr5:70931400-70942400	Weak transcription	Right Ventricle	heart
46	chr5:70931400-70953600	Weak transcription	HSMM	muscle
47	chr5:70931600-70942400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:70931600-70942600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:70931600-70945200	Weak transcription	HMEC	breast
50	chr5:70931600-70947000	Weak transcription	Rectal Smooth Muscle	rectum

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