Variant report

Variant	rs7981902
Chromosome Location	chr13:48470791-48470792
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	chr13:48470064..48472473-chr13:48479999..48482410,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234689	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10397	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs11617143	1.00[CHB][hapmap]
rs13243	0.83[EUR][1000 genomes]
rs2094196	1.00[CHB][hapmap]
rs4331249	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4477588	0.81[EUR][1000 genomes]
rs4942711	0.87[EUR][1000 genomes]
rs56385117	0.83[EUR][1000 genomes]
rs7324919	0.85[EUR][1000 genomes]
rs7326861	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs7331746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7335424	1.00[YRI][hapmap]
rs7335662	1.00[CHB][hapmap]
rs7335869	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7337521	1.00[CHB][hapmap]
rs7339238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7981492	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs7984527	0.91[EUR][1000 genomes]
rs7989765	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7993196	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9534872	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9562772	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9562780	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9562781	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9562784	0.83[EUR][1000 genomes]
rs9562785	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9562791	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9567939	0.86[EUR][1000 genomes]
rs9567944	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9567945	0.99[EUR][1000 genomes]
rs9567946	0.99[EUR][1000 genomes]
rs9567956	0.84[EUR][1000 genomes]
rs9567971	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs9567975	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs9567977	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9567978	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9567982	1.00[CHB][hapmap]
rs9567990	1.00[CHB][hapmap]
rs9567992	1.00[CHB][hapmap]
rs9634811	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7981902	SUCLA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48453800-48471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose
4	chr13:48461000-48472200	Weak transcription	Spleen	Spleen
5	chr13:48461000-48472400	Weak transcription	Lung	lung
6	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
7	chr13:48463600-48474600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:48465000-48484000	Weak transcription	Primary T cells from cord blood	blood
9	chr13:48465200-48478200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:48466400-48471600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:48466600-48471000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:48466600-48471600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:48466800-48471800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:48468000-48471600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:48468600-48485600	Weak transcription	Gastric	stomach
16	chr13:48468800-48479600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr13:48468800-48482400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:48469000-48478200	Weak transcription	Esophagus	oesophagus
19	chr13:48469200-48471400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:48470400-48478000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:48470600-48471600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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