Variant report

Variant	rs13011908
Chromosome Location	chr2:173253033-173253034
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	chr2:173252328..173254724-chr2:173362750..173364595,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12996569	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13005010	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17220266	0.85[EUR][1000 genomes]
rs2884228	0.93[EUR][1000 genomes]
rs34264824	0.81[EUR][1000 genomes]
rs34412908	0.81[EUR][1000 genomes]
rs34653380	0.81[EUR][1000 genomes]
rs35160861	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36091681	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6722935	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415297	1.00[ASN][1000 genomes]
rs7597542	0.87[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13011908	ITGA6	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173239200-173260200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173244600-173254400	Weak transcription	Lung	lung
3	chr2:173246200-173254400	Weak transcription	Fetal Intestine Small	intestine
4	chr2:173246200-173258400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:173246200-173260200	Weak transcription	Right Atrium	heart
6	chr2:173247000-173258200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:173248600-173254600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:173249800-173262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:173250200-173260400	Weak transcription	Thymus	Thymus
10	chr2:173250600-173253600	Weak transcription	Fetal Thymus	thymus
11	chr2:173252200-173254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:173252200-173254600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:173252200-173261400	Weak transcription	Fetal Lung	lung
14	chr2:173252400-173253800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:173252400-173254400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:173252400-173254600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:173252400-173256200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:173252600-173253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:173252600-173253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:173252600-173256400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:173253000-173254200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links