Variant report

Variant	rs1043615
Chromosome Location	chr7:108212353-108212354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:108211992-108212398	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF274	chr7:108212223-108212742	K562	blood:	n/a	n/a
3	POLR2A	chr7:108199426-108221976	K562	blood:	n/a	n/a
4	MXI1	chr7:108207302-108212533	SK-N-SH	brain:	n/a	n/a
5	EP300	chr7:108212199-108212353	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
2	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
3	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
4	chr7:108209600..108213665-chr7:112090307..112092525,3	K562	blood:

No data

Variant related genes	Relation type
THAP5	TF binding region
PNPLA8	TF binding region
ENSG00000135241	Chromatin interaction
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10156002	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253210	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10270723	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10282368	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17426315	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860118	0.85[CEU][hapmap]
rs2041003	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072212	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34668718	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40911	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40913	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40916	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40918	0.85[EUR][1000 genomes]
rs40922	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40927	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40929	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40930	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40933	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40937	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40943	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730324	0.81[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.91[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1043615	C7orf66	cis	cerebellum	SCAN
rs1043615	THAP5	cis	cerebellum	SCAN
rs1043615	DNAJB9	cis	parietal	SCAN
rs1043615	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs1043615	THAP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
2	chr7:108208600-108212400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:108208800-108212400	Active TSS	Right Ventricle	heart
4	chr7:108209400-108213200	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr7:108210400-108212400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:108210600-108212400	Active TSS	Right Atrium	heart
7	chr7:108211000-108212400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:108211200-108212400	Flanking Active TSS	HUVEC	blood vessel
9	chr7:108211200-108214200	Weak transcription	Small Intestine	intestine
10	chr7:108211200-108219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:108211200-108219600	Weak transcription	Lung	lung
12	chr7:108211400-108212400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:108211400-108212400	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:108211400-108212400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr7:108211400-108213400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr7:108211400-108215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:108211400-108216600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:108211400-108217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:108211400-108219400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:108211400-108219600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:108211400-108219600	Weak transcription	Colonic Mucosa	Colon
22	chr7:108211400-108219600	Weak transcription	Esophagus	oesophagus
23	chr7:108211400-108219600	Weak transcription	Ovary	ovary
24	chr7:108211400-108219800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:108211600-108212400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr7:108211600-108212400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr7:108211600-108212400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr7:108211600-108212400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:108211600-108212400	Enhancers	Adipose Nuclei	Adipose
30	chr7:108211600-108212400	Enhancers	Brain Angular Gyrus	brain
31	chr7:108211600-108212400	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:108211600-108212400	Enhancers	Brain Substantia Nigra	brain
33	chr7:108211600-108212400	Enhancers	Rectal Smooth Muscle	rectum
34	chr7:108211600-108212400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr7:108211600-108212400	Flanking Active TSS	NHEK	skin
36	chr7:108211600-108212600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr7:108211600-108212600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr7:108211600-108212600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr7:108211600-108212600	Enhancers	Fetal Lung	lung
40	chr7:108211600-108212600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr7:108211600-108212800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:108211600-108213000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:108211600-108213400	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:108211600-108213600	Weak transcription	HSMMtube	muscle
45	chr7:108211600-108214400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:108211600-108215800	Weak transcription	Thymus	Thymus
47	chr7:108211600-108219200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:108211600-108219200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:108211600-108219400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr7:108211600-108219400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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