Variant report

Variant	rs912397
Chromosome Location	chr13:39848857-39848858
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	chr13:39847798..39849106-chr13:40186090..40186812,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12428000	0.80[ASN][1000 genomes]
rs12583780	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12585448	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12585451	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17059609	0.89[AFR][1000 genomes]
rs17059611	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628476	0.90[EUR][1000 genomes]
rs17628483	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17628519	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2147130	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2324252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324254	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2324255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2324257	1.00[CEU][hapmap]
rs2875296	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2875298	1.00[CEU][hapmap]
rs57251095	0.84[ASN][1000 genomes]
rs58017746	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58305678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563698	0.85[JPT][hapmap]
rs7318557	0.81[JPT][hapmap]
rs74044033	0.84[ASN][1000 genomes]
rs746077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747382	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747384	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990125	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7998423	0.85[ASN][1000 genomes]
rs8253	1.00[CEU][hapmap]

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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv900007	chr13:39801283-39849423	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39847200-39849200	Enhancers	Brain Germinal Matrix	brain
2	chr13:39847800-39849200	Enhancers	Brain Hippocampus Middle	brain
3	chr13:39847800-39850200	Enhancers	Brain Substantia Nigra	brain
4	chr13:39848000-39849000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr13:39848200-39849000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:39848200-39849400	Enhancers	Right Atrium	heart
7	chr13:39848200-39849600	Enhancers	Adipose Nuclei	Adipose
8	chr13:39848200-39849600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr13:39848400-39849000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:39848400-39849000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr13:39848400-39849000	Enhancers	Small Intestine	intestine
12	chr13:39848600-39849000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:39848600-39849400	Enhancers	Left Ventricle	heart
14	chr13:39848600-39849600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:39848800-39849200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr13:39848800-39849600	Enhancers	Brain Angular Gyrus	brain
17	chr13:39848800-39849600	Enhancers	Brain Anterior Caudate	brain
18	chr13:39848800-39849800	Enhancers	Brain Cingulate Gyrus	brain

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