Variant report

Variant	rs10878031
Chromosome Location	chr12:40438429-40438430
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40434942..40437888-chr12:40438406..40442021,3	MCF-7	breast:
2	12:40436818-40441273..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10747989	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs10784338	0.82[CEU][hapmap];0.84[CHB][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10784353	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784356	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784359	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784369	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877990	0.82[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10878049	0.86[CEU][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10878089	0.92[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11174670	0.86[ASN][1000 genomes]
rs11174809	0.83[ASN][1000 genomes]
rs11174812	0.84[ASN][1000 genomes]
rs11174813	0.85[ASN][1000 genomes]
rs11175024	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12813098	0.89[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12823555	0.82[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1482281	0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs1586038	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1600866	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813122	0.94[YRI][hapmap];0.83[ASN][1000 genomes]
rs2128275	0.82[ASN][1000 genomes]
rs2404352	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896825	0.84[ASN][1000 genomes]
rs2896905	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs3925535	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4625545	0.82[ASN][1000 genomes]
rs4767960	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581504	0.89[CEU][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6650226	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs716268	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7313209	0.82[ASN][1000 genomes]
rs7313231	0.82[ASN][1000 genomes]
rs7953129	0.84[CHB][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7954875	0.86[ASN][1000 genomes]
rs7959498	0.82[ASN][1000 genomes]
rs7960662	0.96[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9669240	0.93[CEU][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10878031	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40416600-40441800	Weak transcription	Ovary	ovary
4	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
5	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
6	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:40429400-40441000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:40434000-40441600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:40438400-40440200	Enhancers	Fetal Brain Male	brain

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