Variant report

Variant	rs6696250
Chromosome Location	chr1:151695271-151695272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151693523..151696845-chr1:151699758..151701957,3	MCF-7	breast:
2	chr1:151510464..151513293-chr1:151695020..151697048,2	MCF-7	breast:
3	chr1:151688250..151693808-chr1:151695165..151699893,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159409	Chromatin interaction
ENSG00000178796	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000232536	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];0.89[TSI][hapmap]
rs10888433	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs11204879	0.85[CEU][hapmap];0.89[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.91[TSI][hapmap]
rs2096402	0.96[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs4043740	0.86[CEU][hapmap]
rs41263702	0.81[AMR][1000 genomes]
rs4845339	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs4845542	0.86[JPT][hapmap]
rs6587615	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]
rs6587616	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587617	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6683687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692364	0.81[CEU][hapmap];0.86[TSI][hapmap]
rs8480	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs878775	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[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];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6696250	FLG2	cis	cerebellum	SCAN
rs6696250	BCL9	cis	cerebellum	SCAN
rs6696250	GATAD2B	cis	cerebellum	SCAN
rs6696250	TDRKH	cis	cerebellum	SCAN
rs6696250	SPRR2B	cis	cerebellum	SCAN
rs6696250	CTSK	cis	parietal	SCAN
rs6696250	LYSMD1	cis	parietal	SCAN
rs6696250	LCE1C	cis	parietal	SCAN
rs6696250	TDRKH	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151694400-151695600	Bivalent Enhancer	Fetal Brain Male	brain
2	chr1:151694400-151697200	Weak transcription	A549	lung
3	chr1:151694600-151695400	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:151694600-151696400	Weak transcription	Stomach Mucosa	stomach
5	chr1:151694600-151696600	Weak transcription	Ovary	ovary
6	chr1:151694600-151699200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:151694600-151700000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:151694800-151696600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:151694800-151700000	Weak transcription	Brain Anterior Caudate	brain
10	chr1:151695000-151695400	Bivalent Enhancer	Brain Germinal Matrix	brain
11	chr1:151695000-151696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:151695000-151700400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:151695200-151695400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain

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