Variant report

Variant	rs13175564
Chromosome Location	chr5:60564993-60564994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60564842..60567352-chr5:60626995..60629601,2	K562	blood:
2	chr5:60562038..60564106-chr5:60564910..60567550,2	MCF-7	breast:
3	chr5:60555601..60558433-chr5:60563419..60566177,2	K562	blood:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10037643	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10052765	0.95[ASN][1000 genomes]
rs10062338	0.95[ASN][1000 genomes]
rs10065444	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10071763	0.96[ASN][1000 genomes]
rs10434526	1.00[ASN][1000 genomes]
rs10461467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10471510	0.99[ASN][1000 genomes]
rs10939888	0.96[ASN][1000 genomes]
rs10939890	0.96[ASN][1000 genomes]
rs10939892	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939893	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189426	0.96[ASN][1000 genomes]
rs12518152	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12523278	0.84[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12696979	0.95[ASN][1000 genomes]
rs12696980	0.96[ASN][1000 genomes]
rs34439016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35310874	1.00[ASN][1000 genomes]
rs4129437	0.82[ASN][1000 genomes]
rs4400074	1.00[ASN][1000 genomes]
rs4441832	1.00[ASN][1000 genomes]
rs4540126	0.96[ASN][1000 genomes]
rs4699974	0.95[ASN][1000 genomes]
rs4699975	0.95[ASN][1000 genomes]
rs6864367	0.95[ASN][1000 genomes]
rs6867268	0.99[ASN][1000 genomes]
rs6867417	0.93[ASN][1000 genomes]
rs6882613	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs6885499	0.95[ASN][1000 genomes]
rs6892128	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7448844	0.95[ASN][1000 genomes]
rs7737448	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs9291718	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13175564	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60556000-60570200	Weak transcription	HSMM	muscle
3	chr5:60558000-60566400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:60560000-60569200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:60560400-60569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:60560600-60569000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:60560800-60571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:60561000-60569000	Weak transcription	Brain Substantia Nigra	brain
9	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:60562000-60565400	Weak transcription	Stomach Mucosa	stomach
11	chr5:60563000-60567400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:60564000-60566600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr5:60564400-60565000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:60564400-60565000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:60564400-60565000	Enhancers	HUVEC	blood vessel
16	chr5:60564400-60565600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr5:60564600-60565800	Enhancers	Primary B cells from peripheral blood	blood
18	chr5:60564600-60565800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:60564600-60566000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:60564600-60570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:60564600-60575400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:60564600-60576000	Weak transcription	Psoas Muscle	Psoas
23	chr5:60564800-60565200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:60564800-60565600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:60564800-60565600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:60564800-60566000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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