Variant report

Variant	rs12302398
Chromosome Location	chr12:63334982-63334983
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:63329161..63330688-chr12:63333077..63335873,2	K562	blood:
2	chr12:63331390..63333086-chr12:63334600..63336280,2	MCF-7	breast:
3	chr12:63324965..63327426-chr12:63334327..63336212,2	K562	blood:
4	chr12:63328135..63331466-chr12:63332214..63336504,5	MCF-7	breast:
5	chr12:63327380..63329114-chr12:63332465..63335279,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252660	Chromatin interaction
ENSG00000111110	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10506468	1.00[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11174723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174731	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12301080	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12302449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304611	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12311870	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12314057	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12315582	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12316918	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1250152	0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1666909	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681992	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681993	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1681994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1695023	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17098396	1.00[MEX][hapmap]
rs17098649	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1731665	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173441	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2442110	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2628036	0.97[ASN][1000 genomes]
rs2628038	1.00[ASN][1000 genomes]
rs3858674	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3858675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58389317	0.88[EUR][1000 genomes]
rs58869921	0.88[EUR][1000 genomes]
rs699587	0.88[EUR][1000 genomes]
rs7314488	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315141	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12302398	CXCL11	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63329400-63335200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:63329400-63335200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:63329400-63335200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:63329600-63338600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:63329800-63335400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:63330200-63336000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:63330200-63336200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:63330400-63335400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:63330800-63336200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:63334000-63335400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:63334000-63335600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:63334800-63335400	Enhancers	Brain Hippocampus Middle	brain
13	chr12:63334800-63335400	Enhancers	Brain Substantia Nigra	brain

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