Variant report

Variant	rs6816603
Chromosome Location	chr4:76434873-76434874
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	CHD2	chr4:76434735-76435094	K562	blood:	n/a	n/a
2	CBX3	chr4:76434658-76435271	K562	blood:	n/a	n/a
3	KAP1	chr4:76434690-76435154	HEK293	kidney:	n/a	n/a
4	ZBTB33	chr4:76434711-76435058	K562	blood:	n/a	n/a
5	SETDB1	chr4:76434687-76435207	U2OS	brain:	n/a	n/a
6	ARID3A	chr4:76434574-76434943	K562	blood:	n/a	n/a
7	CBX3	chr4:76434696-76435261	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76433807..76436085-chr4:76437020..76439277,2	MCF-7	breast:
2	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:

Variant related genes	Relation type
THAP6	TF binding region
ENSG00000163743	Chromatin interaction
ENSG00000174796	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10029348	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031553	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046662	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729929	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735018	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112378	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145288	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478174	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580297	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1817387	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841932	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045863	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126855	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28507535	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867920	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867921	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59581284	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535523	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823674	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829753	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833496	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835579	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841882	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664140	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9041	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6816603	THAP6	cis	multi-tissue	Pritchard
rs6816603	ENSG00000174796	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
2	chr4:76395800-76437000	Weak transcription	Lung	lung
3	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
4	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
5	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
8	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
12	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:76411400-76435400	Weak transcription	Small Intestine	intestine
14	chr4:76415400-76435600	Weak transcription	Brain Substantia Nigra	brain
15	chr4:76415400-76436400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:76416600-76436200	Weak transcription	Brain Anterior Caudate	brain
17	chr4:76416600-76437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:76417600-76436800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:76421400-76437000	Weak transcription	Stomach Mucosa	stomach
20	chr4:76424800-76436200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:76424800-76437000	Weak transcription	Psoas Muscle	Psoas
22	chr4:76424800-76437000	Weak transcription	NHLF	lung
23	chr4:76425000-76435000	Strong transcription	HSMM	muscle
24	chr4:76425000-76435600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:76425000-76437000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:76425400-76437000	Weak transcription	Right Ventricle	heart
28	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:76425600-76436600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:76426000-76436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:76427000-76435800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:76427800-76437200	Weak transcription	Fetal Stomach	stomach
33	chr4:76428400-76437400	Weak transcription	A549	lung
34	chr4:76428600-76435400	Weak transcription	NHEK	skin
35	chr4:76428600-76436600	Weak transcription	Brain Germinal Matrix	brain
36	chr4:76429000-76437000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:76430400-76435400	Weak transcription	Ovary	ovary
38	chr4:76430400-76437000	Weak transcription	HSMMtube	muscle
39	chr4:76430600-76435000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:76430600-76436200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:76430600-76436600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:76430600-76436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:76430600-76437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:76430600-76437000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr4:76430600-76437000	Weak transcription	Thymus	Thymus
46	chr4:76430800-76436800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:76430800-76437200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:76430800-76438200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:76431000-76436800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:76431000-76437000	Weak transcription	Fetal Muscle Leg	muscle

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