Variant report

Variant	rs13229488
Chromosome Location	chr7:108126673-108126674
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	chr7:108125833..108127645-chr7:108131948..108133995,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10487859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973105	0.88[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666562	0.81[ASN][1000 genomes]
rs12705470	0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs13227836	0.84[EUR][1000 genomes]
rs13228190	0.86[EUR][1000 genomes]
rs13238841	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs13245101	0.88[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs13307045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13312593	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17155828	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17338441	0.88[EUR][1000 genomes]
rs17338462	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs17423043	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs17423119	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs17424206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs194587	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214913	0.88[EUR][1000 genomes]
rs2214914	0.93[EUR][1000 genomes]
rs2214915	0.94[EUR][1000 genomes]
rs2300048	0.86[EUR][1000 genomes]
rs2300052	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs3202837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33987381	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34218460	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34814097	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34887057	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35372181	0.83[ASN][1000 genomes]
rs35436957	0.86[EUR][1000 genomes]
rs35617326	0.88[EUR][1000 genomes]
rs35880371	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40850	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40854	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40875	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40880	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40882	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40895	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40901	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40915	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40923	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40924	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40925	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40928	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40934	0.81[ASN][1000 genomes]
rs40938	0.81[ASN][1000 genomes]
rs40939	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs40940	0.81[ASN][1000 genomes]
rs40941	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs40944	0.81[ASN][1000 genomes]
rs40945	0.81[ASN][1000 genomes]
rs40946	0.81[ASN][1000 genomes]
rs40947	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs41385644	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4992578	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.85[EUR][1000 genomes]
rs59458537	0.86[EUR][1000 genomes]
rs60398019	0.84[EUR][1000 genomes]
rs60426977	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466233	0.86[EUR][1000 genomes]
rs6466238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66461825	0.88[EUR][1000 genomes]
rs67027479	0.88[EUR][1000 genomes]
rs67694466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949637	0.88[EUR][1000 genomes]
rs6955152	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959023	0.87[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs6976309	0.88[EUR][1000 genomes]
rs6976649	0.87[EUR][1000 genomes]
rs6976659	0.88[EUR][1000 genomes]
rs6976752	0.88[EUR][1000 genomes]
rs6976776	0.88[EUR][1000 genomes]
rs6976804	0.88[EUR][1000 genomes]
rs6978552	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs71213282	0.88[EUR][1000 genomes]
rs71568528	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784170	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs7786947	0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs7790875	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs7806869	0.86[EUR][1000 genomes]
rs7807737	0.88[EUR][1000 genomes]
rs7807941	0.88[EUR][1000 genomes]
rs7811808	0.90[EUR][1000 genomes]
rs9649307	0.88[EUR][1000 genomes]
rs9649308	0.90[EUR][1000 genomes]
rs9785056	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13229488	THAP5	cis	uninvolved skin	skin_eQTL
rs13229488	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs13229488	THAP5	cis	normal skin	skin_eQTL
rs13229488	THAP5	cis	Muscle Skeletal	GTEx
rs13229488	THAP5	cis	Esophagus Muscularis	GTEx
rs13229488	THAP5	cis	multi-tissue	Pritchard
rs13229488	THAP5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
3	chr7:108102400-108137000	Weak transcription	NH-A	brain
4	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
6	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:108106200-108150800	Weak transcription	NHLF	lung
8	chr7:108106600-108127600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr7:108106800-108130000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
11	chr7:108109000-108129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:108109600-108127600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
17	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
18	chr7:108110200-108127800	Weak transcription	Fetal Brain Female	brain
19	chr7:108111000-108137800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr7:108111400-108142200	Strong transcription	Liver	Liver
21	chr7:108111400-108154800	Weak transcription	NHEK	skin
22	chr7:108111600-108138400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:108111600-108142600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:108111800-108143600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr7:108113200-108157000	Weak transcription	Psoas Muscle	Psoas
26	chr7:108113600-108129800	Weak transcription	Hela-S3	cervix
27	chr7:108113600-108140000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:108113800-108150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:108113800-108165800	Weak transcription	Gastric	stomach
30	chr7:108114000-108129800	Weak transcription	Fetal Heart	heart
31	chr7:108114000-108139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
33	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:108114600-108132000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:108114800-108134800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:108115200-108151800	Weak transcription	NHDF-Ad	bronchial
37	chr7:108115800-108132000	Weak transcription	A549	lung
38	chr7:108116400-108141400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:108117200-108150600	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:108117200-108151800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:108118200-108129200	Weak transcription	K562	blood
43	chr7:108119200-108128200	Weak transcription	Fetal Stomach	stomach
44	chr7:108119200-108129400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:108119200-108157600	Weak transcription	Brain Germinal Matrix	brain
46	chr7:108119600-108127600	Weak transcription	Brain Hippocampus Middle	brain
47	chr7:108119600-108127800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:108119600-108131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:108119600-108132000	Weak transcription	Right Ventricle	heart
50	chr7:108119600-108134600	Weak transcription	Primary hematopoietic stem cells	blood

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