Variant report

Variant	rs8042558
Chromosome Location	chr15:75320433-75320434
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:75320400-75320550	AG04449	skin:	n/a	n/a
2	POLR2A	chr15:75320374-75320450	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:119177443..119177955-chr15:75319985..75320485,2	NB4	blood:
2	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
3	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
4	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
5	chr15:75247632..75249513-chr15:75319371..75321803,2	MCF-7	breast:
6	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
7	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
8	chr15:75318584..75321988-chr15:75334747..75339188,4	K562	blood:
9	chr15:75320338..75322055-chr15:75659198..75660857,2	K562	blood:
10	chr15:75319473..75322181-chr17:62205905..62208887,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000178607	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12050628	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911421	0.84[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs12917120	0.81[LWK][hapmap]
rs13056	0.83[ASW][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs1867150	0.81[ASN][1000 genomes]
rs2120019	0.83[ASW][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap]
rs2120020	0.81[ASN][1000 genomes]
rs2304903	0.83[ASW][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs34492112	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35911108	0.81[ASN][1000 genomes]
rs3850093	0.87[JPT][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs4886414	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5020842	0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7175720	0.81[TSI][hapmap]
rs8028632	0.83[ASW][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs8030089	0.86[JPT][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8042558	CDCA7	trans	parietal	SCAN
rs8042558	NEIL1	cis	cerebellum	SCAN
rs8042558	PPCDC	Cis_1M	lymphoblastoid	RTeQTL
rs8042558	ULK3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75316600-75321000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75316600-75321000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:75316600-75321600	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:75316600-75321800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75316600-75336800	Weak transcription	Fetal Brain Female	brain
6	chr15:75316800-75320600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:75316800-75320800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:75316800-75321000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:75316800-75321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:75316800-75321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:75316800-75321400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:75316800-75321400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:75316800-75321400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:75316800-75321400	Weak transcription	HUVEC	blood vessel
15	chr15:75316800-75321600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:75316800-75321600	Weak transcription	HMEC	breast
17	chr15:75316800-75321600	Weak transcription	Osteobl	bone
18	chr15:75316800-75321800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:75316800-75321800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:75316800-75321800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:75316800-75321800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:75316800-75321800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:75316800-75321800	Weak transcription	Esophagus	oesophagus
24	chr15:75316800-75321800	Weak transcription	Gastric	stomach
25	chr15:75316800-75321800	Weak transcription	Left Ventricle	heart
26	chr15:75316800-75321800	Weak transcription	Ovary	ovary
27	chr15:75316800-75321800	Weak transcription	Right Atrium	heart
28	chr15:75316800-75321800	Weak transcription	Right Ventricle	heart
29	chr15:75316800-75321800	Weak transcription	Small Intestine	intestine
30	chr15:75316800-75321800	Weak transcription	HSMM	muscle
31	chr15:75316800-75321800	Weak transcription	NH-A	brain
32	chr15:75316800-75321800	Weak transcription	NHDF-Ad	bronchial
33	chr15:75316800-75321800	Weak transcription	NHLF	lung
34	chr15:75316800-75322000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:75316800-75322000	Weak transcription	Brain Angular Gyrus	brain
36	chr15:75316800-75322000	Weak transcription	Fetal Brain Male	brain
37	chr15:75316800-75322000	Weak transcription	Psoas Muscle	Psoas
38	chr15:75316800-75322000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:75316800-75322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:75316800-75322800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr15:75316800-75338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:75317000-75321800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:75317000-75321800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:75317000-75321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:75317000-75321800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr15:75317000-75322000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:75317200-75321200	Strong transcription	Fetal Stomach	stomach
48	chr15:75317200-75321400	Weak transcription	Primary B cells from cord blood	blood
49	chr15:75317200-75321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:75317200-75321800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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