Variant report

Variant	rs6587615
Chromosome Location	chr1:151699473-151699474
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	chr1:151682201..151684872-chr1:151698617..151700644,2	MCF-7	breast:
2	chr1:151688250..151693808-chr1:151695165..151699893,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240510	Chromatin interaction
ENSG00000159409	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10218531	0.85[CEU][hapmap]
rs10888431	0.85[CEU][hapmap]
rs10888432	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs10888433	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs11204879	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs11204880	0.85[CEU][hapmap]
rs11808761	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs1196350	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs1196462	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs1196466	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs12095851	0.85[CEU][hapmap]
rs12122920	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs12139264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143606	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12758387	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2096402	0.96[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4043740	0.86[CEU][hapmap]
rs41263702	0.83[AMR][1000 genomes]
rs4845339	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs4845542	0.86[JPT][hapmap]
rs6587616	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587617	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683687	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692364	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs6696250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8480	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs878775	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs939592	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6587615	SPRR2B	cis	cerebellum	SCAN
rs6587615	LYSMD1	cis	parietal	SCAN
rs6587615	CTSK	cis	parietal	SCAN
rs6587615	FLG2	cis	cerebellum	SCAN
rs6587615	BCL9	cis	cerebellum	SCAN
rs6587615	GATAD2B	cis	cerebellum	SCAN
rs6587615	LCE1C	cis	parietal	SCAN
rs6587615	TDRKH	cis	parietal	SCAN
rs6587615	TDRKH	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151694600-151700000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:151694800-151700000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:151695000-151700400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:151697000-151701000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:151697200-151700600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:151697200-151700600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:151698200-151701000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr1:151698400-151700000	Enhancers	Fetal Intestine Large	intestine
9	chr1:151698400-151700600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:151698600-151699600	Enhancers	Fetal Intestine Small	intestine
11	chr1:151698800-151700000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151699000-151700000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
13	chr1:151699200-151699800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:151699200-151703800	Enhancers	Fetal Brain Male	brain
15	chr1:151699400-151702400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links