Variant report

Variant	rs40934
Chromosome Location	chr7:108199042-108199043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108197691..108199841-chr7:108209590..108211636,2	K562	blood:
2	chr7:108193337..108196664-chr7:108198034..108202692,4	K562	blood:
3	chr7:108191362..108206184-chr7:108206645..108216261,27	K562	blood:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction
ENSG00000177683	Chromatin interaction
ENSG00000128590	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10487859	0.81[ASN][1000 genomes]
rs11974559	0.86[ASN][1000 genomes]
rs11981670	0.81[ASN][1000 genomes]
rs12666562	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229488	0.81[ASN][1000 genomes]
rs17155828	0.81[ASN][1000 genomes]
rs17424206	0.81[ASN][1000 genomes]
rs194587	0.81[ASN][1000 genomes]
rs3202837	0.81[ASN][1000 genomes]
rs34814097	0.81[ASN][1000 genomes]
rs34887057	0.81[ASN][1000 genomes]
rs35372181	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35880371	0.81[ASN][1000 genomes]
rs3763457	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40843	0.81[ASN][1000 genomes]
rs40845	0.81[ASN][1000 genomes]
rs40850	0.81[ASN][1000 genomes]
rs40854	0.81[ASN][1000 genomes]
rs40872	0.86[ASN][1000 genomes]
rs40875	0.86[ASN][1000 genomes]
rs40878	0.86[ASN][1000 genomes]
rs40880	0.86[ASN][1000 genomes]
rs40882	0.81[ASN][1000 genomes]
rs40885	0.86[ASN][1000 genomes]
rs40886	0.86[ASN][1000 genomes]
rs40895	0.86[ASN][1000 genomes]
rs40899	0.86[ASN][1000 genomes]
rs40900	0.86[ASN][1000 genomes]
rs40901	0.86[ASN][1000 genomes]
rs40902	0.86[ASN][1000 genomes]
rs40908	0.86[ASN][1000 genomes]
rs40910	0.86[ASN][1000 genomes]
rs40912	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40914	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40915	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40919	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40921	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40923	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40924	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40925	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40926	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40928	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40931	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40932	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40936	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs40938	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40939	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40940	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40941	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs40944	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40945	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40946	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40947	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40948	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60426977	0.81[ASN][1000 genomes]
rs6466238	0.81[ASN][1000 genomes]
rs67694466	0.81[ASN][1000 genomes]
rs6947492	0.81[ASN][1000 genomes]
rs6955152	0.81[ASN][1000 genomes]
rs71568528	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40934	THAP5	cis	Muscle Skeletal	GTEx
rs40934	THAP5	cis	Esophagus Muscularis	GTEx
rs40934	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108190200-108201400	Weak transcription	HSMMtube	muscle
2	chr7:108191400-108204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:108195600-108208400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:108197600-108208600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:108197800-108208600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:108198000-108201200	Weak transcription	Placenta	Placenta
7	chr7:108198000-108201600	Weak transcription	HSMM	muscle
8	chr7:108198000-108204200	Weak transcription	Fetal Thymus	thymus
9	chr7:108198000-108208400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:108198400-108207800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:108198400-108208400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:108198600-108199400	Weak transcription	A549	lung
13	chr7:108198600-108200800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:108198600-108200800	Weak transcription	Ovary	ovary
15	chr7:108198600-108202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:108198600-108202000	Weak transcription	Primary B cells from cord blood	blood
17	chr7:108198600-108202000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:108198600-108203000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:108198600-108204200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:108198600-108204200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr7:108198600-108204600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:108198600-108204800	Weak transcription	Dnd41	blood
23	chr7:108198600-108207400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:108198600-108208600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:108198600-108208600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:108198600-108208600	Weak transcription	Fetal Brain Male	brain
27	chr7:108198600-108208600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:108198600-108208600	Weak transcription	Thymus	Thymus
29	chr7:108198800-108201800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:108198800-108202400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr7:108198800-108204200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:108198800-108204200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:108198800-108204400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:108198800-108204400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr7:108198800-108205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:108198800-108206000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:108199000-108202200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr7:108199000-108207600	Weak transcription	Duodenum Mucosa	Duodenum

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