Variant report

Variant	rs6535523
Chromosome Location	chr4:76462224-76462225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76460814..76463695-chr4:76466513..76469151,2	K562	blood:
2	chr4:76440275..76442057-chr4:76460555..76462360,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10029348	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10031553	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10034359	1.00[YRI][hapmap]
rs1046662	0.92[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11728327	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729286	1.00[YRI][hapmap]
rs11729290	0.84[GIH][hapmap]
rs11729929	0.83[EUR][1000 genomes]
rs11730978	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11735018	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13112378	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119499	1.00[YRI][hapmap]
rs13136001	1.00[YRI][hapmap]
rs13145288	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1395359	0.88[CEU][hapmap]
rs1478174	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1580297	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1600100	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1817387	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1841932	0.92[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1841934	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045863	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2126855	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28507535	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2867920	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2867921	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3853183	1.00[ASW][hapmap]
rs59581284	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6815241	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816603	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829753	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833496	0.88[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6835579	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6841171	0.88[CEU][hapmap]
rs6841882	0.92[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7661659	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664140	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7698352	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs786688	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs9041	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998529	0.82[GIH][hapmap];1.00[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6535523	THAP6	cis	lymphoblastoid	seeQTL
rs6535523	THAP6	cis	multi-tissue	Pritchard
rs6535523	CCNI	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
2	chr4:76440400-76473200	Weak transcription	Gastric	stomach
3	chr4:76443400-76470200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:76444400-76471800	Weak transcription	Fetal Brain Male	brain
5	chr4:76451600-76474400	Weak transcription	Psoas Muscle	Psoas
6	chr4:76452600-76468000	Weak transcription	NHLF	lung
7	chr4:76452600-76477400	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:76453200-76473600	Weak transcription	Brain Angular Gyrus	brain
9	chr4:76455000-76469400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:76455000-76470200	Weak transcription	Brain Substantia Nigra	brain
11	chr4:76455000-76470800	Weak transcription	NHDF-Ad	bronchial
12	chr4:76456000-76473000	Weak transcription	HepG2	liver
13	chr4:76456400-76471600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:76456600-76467400	Weak transcription	HMEC	breast
15	chr4:76456600-76467400	Weak transcription	Osteobl	bone
16	chr4:76456600-76471000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:76456600-76473200	Weak transcription	Fetal Heart	heart
18	chr4:76456800-76464200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:76456800-76467600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:76456800-76467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:76456800-76470000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:76456800-76472400	Weak transcription	Brain Anterior Caudate	brain
23	chr4:76456800-76474400	Weak transcription	HSMMtube	muscle
24	chr4:76457000-76468400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:76457000-76470200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:76457000-76470800	Weak transcription	HSMM	muscle
27	chr4:76457000-76471800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:76457000-76474400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:76458000-76464600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:76458000-76470200	Weak transcription	Right Ventricle	heart
31	chr4:76458200-76464400	Weak transcription	Ovary	ovary
32	chr4:76458200-76465000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:76458200-76467400	Weak transcription	Primary B cells from cord blood	blood
34	chr4:76458200-76468000	Weak transcription	Left Ventricle	heart
35	chr4:76458200-76470000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:76458200-76470200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:76458200-76470200	Weak transcription	Aorta	Aorta
38	chr4:76458200-76470200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:76458200-76472000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:76458200-76472000	Weak transcription	Thymus	Thymus
41	chr4:76458200-76472600	Weak transcription	Pancreas	Pancrea
42	chr4:76458200-76474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:76458400-76464800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:76458400-76465800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:76458400-76467800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:76458400-76470000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:76458400-76470000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:76458400-76480800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:76458600-76464000	Weak transcription	Liver	Liver
50	chr4:76458800-76462800	Weak transcription	Placenta	Placenta

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