Variant report

Variant	rs60426977
Chromosome Location	chr7:108117283-108117284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108089080..108090844-chr7:108114077..108117502,3	K562	blood:
2	chr7:108116534..108119287-chr7:108165768..108167593,2	K562	blood:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10487859	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973105	0.86[EUR][1000 genomes]
rs11974559	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11981670	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666562	0.81[ASN][1000 genomes]
rs12705470	0.86[EUR][1000 genomes]
rs13227836	0.83[EUR][1000 genomes]
rs13228190	0.84[EUR][1000 genomes]
rs13229488	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238841	0.84[EUR][1000 genomes]
rs13245101	0.86[EUR][1000 genomes]
rs13245242	0.86[EUR][1000 genomes]
rs13307045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13312593	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17155828	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17338441	0.86[EUR][1000 genomes]
rs17338462	0.86[EUR][1000 genomes]
rs17423043	0.86[EUR][1000 genomes]
rs17423119	0.86[EUR][1000 genomes]
rs17424206	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194587	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214913	0.86[EUR][1000 genomes]
rs2214914	0.92[EUR][1000 genomes]
rs2214915	0.92[EUR][1000 genomes]
rs2300048	0.84[EUR][1000 genomes]
rs2300052	0.86[EUR][1000 genomes]
rs3202837	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33987381	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34218460	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34814097	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34887057	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35372181	0.83[ASN][1000 genomes]
rs35436957	0.84[EUR][1000 genomes]
rs35617326	0.86[EUR][1000 genomes]
rs35880371	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40843	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40845	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40850	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40854	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40872	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40875	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40878	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40880	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40882	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40885	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40886	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40895	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40899	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40900	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40901	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40902	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40908	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40910	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40915	0.86[ASN][1000 genomes]
rs40923	0.86[ASN][1000 genomes]
rs40924	0.86[ASN][1000 genomes]
rs40925	0.86[ASN][1000 genomes]
rs40928	0.86[ASN][1000 genomes]
rs40934	0.81[ASN][1000 genomes]
rs40938	0.81[ASN][1000 genomes]
rs40939	0.81[ASN][1000 genomes]
rs40940	0.81[ASN][1000 genomes]
rs40941	0.81[ASN][1000 genomes]
rs40944	0.81[ASN][1000 genomes]
rs40945	0.81[ASN][1000 genomes]
rs40946	0.81[ASN][1000 genomes]
rs40947	0.81[ASN][1000 genomes]
rs41385644	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4992578	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.83[EUR][1000 genomes]
rs59458537	0.84[EUR][1000 genomes]
rs60398019	0.83[EUR][1000 genomes]
rs6466233	0.84[EUR][1000 genomes]
rs6466238	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66461825	0.86[EUR][1000 genomes]
rs67027479	0.86[EUR][1000 genomes]
rs67694466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947492	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949637	0.86[EUR][1000 genomes]
rs6955152	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959023	0.85[EUR][1000 genomes]
rs6967368	0.93[EUR][1000 genomes]
rs6976309	0.86[EUR][1000 genomes]
rs6976649	0.85[EUR][1000 genomes]
rs6976659	0.86[EUR][1000 genomes]
rs6976752	0.86[EUR][1000 genomes]
rs6976776	0.86[EUR][1000 genomes]
rs6976804	0.86[EUR][1000 genomes]
rs6978552	0.84[EUR][1000 genomes]
rs71213282	0.86[EUR][1000 genomes]
rs71568528	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784170	0.84[EUR][1000 genomes]
rs7786947	0.86[EUR][1000 genomes]
rs7790875	0.84[EUR][1000 genomes]
rs7806869	0.84[EUR][1000 genomes]
rs7807737	0.86[EUR][1000 genomes]
rs7807941	0.86[EUR][1000 genomes]
rs7811808	0.88[EUR][1000 genomes]
rs9649307	0.86[EUR][1000 genomes]
rs9649308	0.88[EUR][1000 genomes]
rs9785056	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][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	esv2753284	chr7:108105345-108130214	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs60426977	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs60426977	THAP5	cis	Muscle Skeletal	GTEx
rs60426977	THAP5	cis	Heart Left Ventricle	GTEx
rs60426977	THAP5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
2	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:108101000-108119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
5	chr7:108102400-108137000	Weak transcription	NH-A	brain
6	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:108102600-108118200	Weak transcription	Fetal Muscle Leg	muscle
8	chr7:108102800-108126400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
10	chr7:108104800-108117400	Weak transcription	Dnd41	blood
11	chr7:108105600-108117800	Weak transcription	Thymus	Thymus
12	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:108106200-108150800	Weak transcription	NHLF	lung
14	chr7:108106600-108127600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr7:108106800-108130000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
17	chr7:108108600-108122000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:108108800-108118200	Weak transcription	Right Ventricle	heart
19	chr7:108108800-108118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:108109000-108119200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:108109000-108126400	Weak transcription	HUVEC	blood vessel
22	chr7:108109000-108129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:108109600-108127600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
28	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
29	chr7:108110000-108118000	Weak transcription	Ovary	ovary
30	chr7:108110200-108127800	Weak transcription	Fetal Brain Female	brain
31	chr7:108110800-108121000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:108111000-108137800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr7:108111200-108117600	Weak transcription	Fetal Lung	lung
34	chr7:108111400-108142200	Strong transcription	Liver	Liver
35	chr7:108111400-108154800	Weak transcription	NHEK	skin
36	chr7:108111600-108118600	Weak transcription	HMEC	breast
37	chr7:108111600-108119400	Weak transcription	HSMM	muscle
38	chr7:108111600-108138400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:108111600-108142600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr7:108111800-108143600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:108112000-108118000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:108112000-108118000	Weak transcription	Lung	lung
43	chr7:108112600-108118000	Weak transcription	Fetal Intestine Small	intestine
44	chr7:108112800-108118000	Weak transcription	Brain Germinal Matrix	brain
45	chr7:108113000-108119000	Weak transcription	Brain Angular Gyrus	brain
46	chr7:108113200-108118200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr7:108113200-108122200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:108113200-108157000	Weak transcription	Psoas Muscle	Psoas
49	chr7:108113600-108118000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:108113600-108118600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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