Variant report

Variant	rs7698352
Chromosome Location	chr4:76409077-76409078
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10029348	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10031553	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1046662	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11728327	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11730978	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11735018	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11935932	0.82[EUR][1000 genomes]
rs13112378	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13145288	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1351092	0.86[EUR][1000 genomes]
rs1389443	0.86[EUR][1000 genomes]
rs1395359	0.85[CEU][hapmap]
rs1478174	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1564174	0.85[EUR][1000 genomes]
rs1580297	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1600100	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676917	0.86[EUR][1000 genomes]
rs1817387	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1841932	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841934	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2045863	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2126855	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28507535	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2867920	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867921	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59581284	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535523	0.82[ASN][1000 genomes]
rs6815241	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6816603	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6823674	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6829753	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6833496	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6835579	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6841171	0.85[CEU][hapmap]
rs6841882	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7664140	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs786682	0.86[EUR][1000 genomes]
rs786684	0.86[EUR][1000 genomes]
rs786688	0.88[CEU][hapmap]
rs9041	0.84[AMR][1000 genomes];0.82[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
rs7698352	THAP6	cis	multi-tissue	Pritchard
rs7698352	THAP6	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
3	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
4	chr4:76395800-76437000	Weak transcription	Lung	lung
5	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
6	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
8	chr4:76397200-76414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:76398200-76415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
15	chr4:76400800-76409200	Weak transcription	Thymus	Thymus
16	chr4:76401000-76410800	Weak transcription	HSMMtube	muscle
17	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
18	chr4:76401200-76409200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:76401200-76410800	Weak transcription	Stomach Mucosa	stomach
20	chr4:76401200-76411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:76401800-76412400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:76402000-76411600	Strong transcription	HSMM	muscle
23	chr4:76402000-76412200	Strong transcription	Adipose Nuclei	Adipose
24	chr4:76402000-76418600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:76402200-76409600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:76402200-76412200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:76402200-76412200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:76402200-76422000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:76402200-76423000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:76402200-76425800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:76402400-76409600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:76402400-76409800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:76402400-76411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:76402400-76412000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr4:76402400-76418400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:76402400-76418800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr4:76402400-76419200	Strong transcription	Liver	Liver
38	chr4:76402400-76425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:76402600-76411400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:76402600-76411400	Strong transcription	Primary B cells from cord blood	blood
41	chr4:76402600-76423200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:76402800-76411600	Weak transcription	Fetal Intestine Small	intestine
43	chr4:76402800-76417600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:76403000-76411000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:76403000-76423800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:76403600-76411200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr4:76403600-76418800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:76403800-76409600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:76403800-76410000	Strong transcription	HUVEC	blood vessel
50	chr4:76403800-76412200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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