Variant report

Variant	rs5030783
Chromosome Location	chr15:40984389-40984390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr15:40983971-40984406	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:40984244-40984560	K562	blood:	n/a	n/a
3	POLR2A	chr15:40984246-40984428	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr15:40984276-40984698	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40983418..40985214-chr15:40986954..40989432,2	K562	blood:
2	chr15:40982126..40985382-chr15:40985435..40988081,4	MCF-7	breast:

Variant related genes	Relation type
RAD51	TF binding region
ENSG00000051180	Chromatin interaction
ENSG00000245849	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051482	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10851396	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs11070279	0.87[CEU][hapmap]
rs11070290	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852479	0.84[AMR][1000 genomes]
rs11855517	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11857247	0.87[CEU][hapmap]
rs12148185	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12898552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12906755	0.82[CEU][hapmap]
rs12907448	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes]
rs12907984	0.82[AMR][1000 genomes]
rs12908114	0.87[CEU][hapmap]
rs12908443	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12910784	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12915563	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs12916323	0.88[CEU][hapmap]
rs1453183	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs17747399	0.82[AMR][1000 genomes]
rs2010300	0.92[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs2289219	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2304583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899000	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs34621344	0.82[EUR][1000 genomes]
rs34988257	0.86[EUR][1000 genomes]
rs35884042	0.82[AMR][1000 genomes]
rs36094699	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3759796	0.82[EUR][1000 genomes]
rs4457966	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs45592734	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62019934	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025458	0.92[CEU][hapmap]
rs8028910	0.88[CEU][hapmap]
rs8031427	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038396	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9806410	0.91[CEU][hapmap]
rs999197	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs5030783	C15orf57	cis	Adipose Subcutaneous	GTEx
rs5030783	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs5030783	C15orf57	cis	Stomach	GTEx
rs5030783	CCDC32	cis	multi-tissue	Pritchard
rs5030783	RP11-111A22.1	cis	lung	GTEx
rs5030783	C15orf57	cis	Artery Aorta	GTEx
rs5030783	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs5030783	C15orf57	cis	Esophagus Mucosa	GTEx
rs5030783	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs5030783	MGC20481	cis	multi-tissue	Pritchard
rs5030783	C15orf57	cis	Cerebellum	GTEx
rs5030783	C15orf57	cis	Esophagus Muscularis	GTEx
rs5030783	C15orf57	cis	Artery Tibial	GTEx
rs5030783	C15orf57	cis	Nerve Tibial	GTEx
rs5030783	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs5030783	ZFYVE19	cis	multi-tissue	Pritchard
rs5030783	C15orf57	cis	lung	GTEx
rs5030783	C15orf57	cis	Lymphoblastoid	GTEx
rs5030783	RP11-111A22.1	cis	Artery Tibial	GTEx
rs5030783	C15orf57	cis	Muscle Skeletal	GTEx
rs5030783	RAD51	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40913800-40986000	Weak transcription	A549	lung
2	chr15:40971200-40985800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr15:40971600-40985600	Weak transcription	Dnd41	blood
4	chr15:40971600-40985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:40971800-40985800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:40972400-40984600	Weak transcription	Placenta	Placenta
7	chr15:40973200-40985600	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40973400-40985800	Weak transcription	GM12878-XiMat	blood
9	chr15:40977000-40985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:40977200-40985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:40977400-40985800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:40977400-40986200	Weak transcription	Esophagus	oesophagus
13	chr15:40978000-40985800	Weak transcription	Gastric	stomach
14	chr15:40978000-40986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:40978200-40985800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:40978200-40986000	Weak transcription	HSMMtube	muscle
17	chr15:40978400-40984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:40978600-40986000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:40978600-40986000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:40979000-40986000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:40979400-40986000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:40979400-40986000	Weak transcription	HUVEC	blood vessel
23	chr15:40979600-40984400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:40979600-40986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:40979800-40985800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:40979800-40986000	Weak transcription	Left Ventricle	heart
27	chr15:40980400-40985600	Weak transcription	Pancreas	Pancrea
28	chr15:40980400-40985800	Weak transcription	Fetal Brain Male	brain
29	chr15:40980400-40986000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:40980800-40986000	Weak transcription	NHLF	lung
31	chr15:40981000-40986000	Weak transcription	NHDF-Ad	bronchial
32	chr15:40981200-40984600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr15:40981200-40986000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:40981200-40986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:40981400-40986200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:40981400-40986200	Weak transcription	Psoas Muscle	Psoas
37	chr15:40981600-40985800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:40981600-40986000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:40981800-40984600	Weak transcription	Fetal Brain Female	brain
40	chr15:40981800-40985800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr15:40981800-40985800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:40982000-40985800	Weak transcription	NHEK	skin
43	chr15:40982000-40986000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:40982000-40986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:40982400-40984400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:40982400-40986000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:40982400-40986000	Weak transcription	Brain Germinal Matrix	brain
48	chr15:40982400-40986000	Weak transcription	Hela-S3	cervix
49	chr15:40982400-40986200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr15:40982400-40986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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