Variant report

Variant	rs6690084
Chromosome Location	chr1:47794706-47794707
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	chr1:47779023..47781686-chr1:47794382..47795947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10789507	0.81[MEX][hapmap]
rs11211508	1.00[ASW][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap]
rs11211520	1.00[YRI][hapmap]
rs11582877	1.00[YRI][hapmap]
rs12026822	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12035995	0.83[GIH][hapmap]
rs12039270	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12039726	1.00[YRI][hapmap]
rs17418545	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2249665	0.90[MEX][hapmap]
rs2742101	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2798349	0.95[MEX][hapmap]
rs2821097	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088062	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs3125635	0.86[MEX][hapmap]
rs3125644	0.86[MEX][hapmap]
rs3814005	0.83[GIH][hapmap]
rs4600090	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4926858	0.83[GIH][hapmap]
rs56881474	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6660321	1.00[YRI][hapmap]
rs6666370	0.83[GIH][hapmap]
rs6697248	0.86[MEX][hapmap]
rs7532148	1.00[ASW][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap]
rs7534571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]

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	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6690084	CMPK1	cis	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47780600-47798000	Weak transcription	HSMMtube	muscle
3	chr1:47780800-47797800	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:47789800-47796200	Weak transcription	K562	blood
5	chr1:47790200-47797400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:47790600-47797000	Weak transcription	Pancreas	Pancrea
7	chr1:47790600-47797800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:47791800-47797600	Weak transcription	Fetal Intestine Small	intestine
9	chr1:47791800-47798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:47792400-47797600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:47792400-47797800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:47792600-47795000	Weak transcription	Fetal Stomach	stomach
13	chr1:47792600-47798000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:47792600-47798400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:47792800-47798600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:47793200-47797600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:47793200-47797800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:47793400-47796600	Weak transcription	Esophagus	oesophagus
19	chr1:47793600-47797400	Weak transcription	Fetal Brain Female	brain
20	chr1:47793600-47798000	Weak transcription	Left Ventricle	heart
21	chr1:47794000-47798200	Weak transcription	Ovary	ovary
22	chr1:47794200-47794800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:47794200-47797800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:47794200-47798000	Weak transcription	Liver	Liver
25	chr1:47794400-47795000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:47794400-47795200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:47794600-47798000	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links