Variant report

Variant	rs12030262
Chromosome Location	chr1:161000464-161000465
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160999454..161004323-chr1:161006023..161009248,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215845	Chromatin interaction
ENSG00000270149	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1023115	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs12723902	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12743772	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2246139	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2256633	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2481072	0.85[ASN][1000 genomes]
rs2483144	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2483148	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28365978	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2990700	0.81[ASN][1000 genomes]
rs2990701	0.84[ASN][1000 genomes]
rs2990704	0.85[ASN][1000 genomes]
rs2990705	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007156	0.84[ASN][1000 genomes]
rs3007157	0.85[ASN][1000 genomes]
rs4656975	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530765	0.83[ASN][1000 genomes]
rs7546890	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9427367	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12030262	TSTD1,F11R	cis	brain	BrainEAC
rs12030262	MNDA	cis	cerebellum	SCAN
rs12030262	ASH1L	cis	cerebellum	SCAN
rs12030262	RAB25	cis	parietal	SCAN
rs12030262	OLFML2B	cis	cerebellum	SCAN
rs12030262	ARHGEF11	cis	cerebellum	SCAN
rs12030262	USF1	cis	multi-tissue	Pritchard
rs12030262	F11R	cis	Thyroid	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160991200-161007800	Weak transcription	HSMMtube	muscle
2	chr1:160991600-161002400	Weak transcription	Ovary	ovary
3	chr1:160991600-161007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:160991800-161004600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:160991800-161005200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:160991800-161007600	Weak transcription	Thymus	Thymus
7	chr1:160991800-161007800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:160992000-161001600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:160992000-161002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:160992000-161002200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:160992000-161004600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:160992000-161007000	Weak transcription	Fetal Intestine Small	intestine
13	chr1:160992200-161008000	Weak transcription	HUVEC	blood vessel
14	chr1:160992400-161002400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:160992800-161002200	Weak transcription	NHEK	skin
16	chr1:160995600-161002000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:160995600-161002000	Weak transcription	K562	blood
18	chr1:160995600-161002600	Weak transcription	HSMM	muscle
19	chr1:160997200-161008000	Weak transcription	A549	lung
20	chr1:160997400-161001800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:160999600-161004400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:160999800-161000800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:161000400-161002000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links