Variant report

Variant	rs530305
Chromosome Location	chr15:43495900-43495901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43495127..43497089-chr15:43559128..43561909,2	K562	blood:
2	chr15:43486542..43488730-chr15:43494665..43496385,2	K562	blood:
3	chr15:43485802..43488826-chr15:43494218..43496836,3	K562	blood:
4	chr15:43492792..43496701-chr15:43499050..43501671,3	K562	blood:
5	chr15:43478405..43480682-chr15:43493696..43496696,3	K562	blood:

Variant related genes	Relation type
ENSG00000166947	Chromatin interaction
ENSG00000261679	Chromatin interaction
ENSG00000166946	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11070386	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs11070391	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11070396	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070397	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11070398	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11630595	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs11855754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592725	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1462856	0.89[CEU][hapmap];0.81[GIH][hapmap]
rs16957511	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1834643	0.97[EUR][1000 genomes]
rs2042742	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412752	0.82[JPT][hapmap]
rs28585036	0.92[ASW][hapmap];0.86[CEU][hapmap];0.91[LWK][hapmap]
rs28756768	0.94[EUR][1000 genomes]
rs2899077	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2947019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34646108	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736054	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs3784267	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784268	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4573908	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs4924704	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs4924709	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494863	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs495286	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499280	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538218	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540587	0.88[CEU][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493076	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs6493077	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs6493078	0.89[ASN][1000 genomes]
rs7174915	0.89[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7183814	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8027371	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[ASN][1000 genomes]
rs8027733	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs9652444	0.84[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs530305	DAPK1	trans	lymphoblastoid	seeQTL
rs530305	GMFG	trans	lymphoblastoid	seeQTL
rs530305	C15orf63	cis	lymphoblastoid	seeQTL
rs530305	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs530305	CCNDBP1	cis	multi-tissue	Pritchard
rs530305	TGM5	cis	lymphoblastoid	seeQTL
rs530305	ELL3	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43478600-43496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43482800-43496400	Weak transcription	A549	lung
3	chr15:43485000-43496400	Weak transcription	Stomach Mucosa	stomach
4	chr15:43485200-43496400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:43487400-43496000	Weak transcription	HMEC	breast
6	chr15:43487400-43496800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:43487600-43496400	Weak transcription	HUVEC	blood vessel
8	chr15:43488200-43496200	Weak transcription	Hela-S3	cervix
9	chr15:43489400-43496200	Weak transcription	Left Ventricle	heart
10	chr15:43489600-43496000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:43489600-43496400	Weak transcription	Psoas Muscle	Psoas
12	chr15:43489800-43496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:43489800-43496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:43489800-43496200	Weak transcription	Pancreas	Pancrea
15	chr15:43489800-43496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:43489800-43496400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:43489800-43496400	Weak transcription	Right Ventricle	heart
18	chr15:43489800-43496600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:43489800-43496600	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:43489800-43496800	Weak transcription	HSMM	muscle
21	chr15:43489800-43503000	Weak transcription	K562	blood
22	chr15:43489800-43513200	Weak transcription	Right Atrium	heart
23	chr15:43490000-43496200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:43490000-43496400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:43490000-43496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:43490000-43496400	Weak transcription	Thymus	Thymus
27	chr15:43490200-43496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:43490400-43498800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:43490600-43496400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:43490600-43496400	Weak transcription	Adipose Nuclei	Adipose
31	chr15:43490600-43496800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:43490600-43497200	Weak transcription	Primary B cells from cord blood	blood
33	chr15:43491200-43498800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:43491600-43496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:43492600-43501000	Weak transcription	Spleen	Spleen
36	chr15:43494400-43496600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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