Variant report

Variant	rs159536
Chromosome Location	chr5:60447422-60447423
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	chr5:60446341..60452214-chr5:60453805..60459863,10	K562	blood:
2	chr5:60444410..60449670-chr5:60456383..60459934,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10805374	0.82[EUR][1000 genomes]
rs10939879	0.85[EUR][1000 genomes]
rs10939881	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11739952	0.85[EUR][1000 genomes]
rs12516995	0.84[EUR][1000 genomes]
rs12517310	0.84[EUR][1000 genomes]
rs12518404	0.94[EUR][1000 genomes]
rs12518792	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652830	0.82[EUR][1000 genomes]
rs12653132	0.92[EUR][1000 genomes]
rs12655209	0.84[EUR][1000 genomes]
rs1382917	0.85[EUR][1000 genomes]
rs1460961	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471488	0.81[EUR][1000 genomes]
rs1479645	0.84[EUR][1000 genomes]
rs1526896	0.92[EUR][1000 genomes]
rs159535	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17419290	0.87[EUR][1000 genomes]
rs17444495	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1983484	0.91[EUR][1000 genomes]
rs2049579	0.91[EUR][1000 genomes]
rs28436304	0.85[EUR][1000 genomes]
rs2898309	0.82[EUR][1000 genomes]
rs34608	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34619	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34625	0.83[AFR][1000 genomes]
rs4642318	0.85[EUR][1000 genomes]
rs4647052	0.84[EUR][1000 genomes]
rs4700402	0.82[EUR][1000 genomes]
rs4700404	0.85[EUR][1000 genomes]
rs4700407	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55738840	0.84[EUR][1000 genomes]
rs55814394	0.84[EUR][1000 genomes]
rs56025209	0.91[EUR][1000 genomes]
rs56031340	0.85[EUR][1000 genomes]
rs56284222	0.92[EUR][1000 genomes]
rs56350217	0.82[EUR][1000 genomes]
rs58646987	0.85[EUR][1000 genomes]
rs61017995	0.82[EUR][1000 genomes]
rs62365455	0.85[EUR][1000 genomes]
rs62365458	0.82[EUR][1000 genomes]
rs62367862	0.82[EUR][1000 genomes]
rs62367872	0.85[EUR][1000 genomes]
rs62367878	0.81[EUR][1000 genomes]
rs62367879	0.82[EUR][1000 genomes]
rs62367885	0.83[EUR][1000 genomes]
rs62367903	0.87[EUR][1000 genomes]
rs6449512	0.81[EUR][1000 genomes]
rs67490467	0.85[EUR][1000 genomes]
rs68104763	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726824	0.85[EUR][1000 genomes]
rs72757187	0.85[EUR][1000 genomes]
rs72759206	0.85[EUR][1000 genomes]
rs72759215	0.92[EUR][1000 genomes]
rs7709522	0.85[EUR][1000 genomes]
rs7713481	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7714396	0.86[EUR][1000 genomes]
rs7723901	0.82[EUR][1000 genomes]
rs7734205	0.87[EUR][1000 genomes]
rs7737276	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868791	0.82[EUR][1000 genomes]
rs888799	0.91[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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs159536	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs159536	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60398800-60453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60417200-60449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:60428600-60452000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:60434400-60449600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:60436000-60457600	Weak transcription	Esophagus	oesophagus
6	chr5:60438000-60455400	Weak transcription	Fetal Brain Female	brain
7	chr5:60438600-60452000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:60438600-60452000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:60438600-60455600	Weak transcription	Fetal Kidney	kidney
10	chr5:60438800-60455800	Weak transcription	Brain Germinal Matrix	brain
11	chr5:60439000-60451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:60440400-60457400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:60440600-60455800	Weak transcription	Left Ventricle	heart
14	chr5:60441000-60448000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:60441000-60455800	Weak transcription	Pancreas	Pancrea
16	chr5:60442400-60455800	Weak transcription	NHLF	lung
17	chr5:60443800-60451800	Weak transcription	A549	lung
18	chr5:60445000-60452200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:60445000-60452400	Weak transcription	HSMM	muscle
20	chr5:60445400-60452000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:60445400-60455000	Weak transcription	Fetal Lung	lung
22	chr5:60445600-60455600	Weak transcription	Primary T cells from cord blood	blood
23	chr5:60446200-60454600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr5:60446400-60451200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:60446400-60451800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:60446400-60452400	Weak transcription	NHEK	skin
27	chr5:60446600-60457400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:60446800-60456600	Weak transcription	Fetal Stomach	stomach
29	chr5:60447000-60451600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:60447000-60452000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:60447400-60457400	Weak transcription	Ovary	ovary

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