Variant report

Variant	rs9041
Chromosome Location	chr4:76454850-76454851
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76438334..76441776-chr4:76453885..76456966,3	MCF-7	breast:
2	chr4:76443470..76446392-chr4:76452432..76455084,2	K562	blood:

Variant related genes	Relation type
ENSG00000163743	Chromatin interaction
ENSG00000174796	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10029348	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10031553	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1046662	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11728327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729929	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11730978	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735018	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13112378	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13145288	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1478174	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1580297	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1600100	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1817387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1841932	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1841934	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045863	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126855	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28507535	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867920	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2867921	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59581284	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535523	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815241	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816603	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6823674	0.80[AMR][1000 genomes]
rs6829753	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6833496	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6835579	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841882	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7661659	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7664140	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7698352	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9041	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76455200	Weak transcription	Esophagus	oesophagus
2	chr4:76440400-76456200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:76440400-76456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:76440400-76458000	Weak transcription	Spleen	Spleen
5	chr4:76440400-76458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
7	chr4:76440400-76473200	Weak transcription	Gastric	stomach
8	chr4:76440600-76455400	Weak transcription	Right Ventricle	heart
9	chr4:76440800-76455800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:76440800-76455800	Weak transcription	Thymus	Thymus
11	chr4:76440800-76456000	Weak transcription	Pancreas	Pancrea
12	chr4:76440800-76457400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:76440800-76458600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:76441000-76456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:76441400-76456800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:76441400-76457400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:76441600-76456400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:76441600-76457400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:76441600-76457600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:76441600-76458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:76441600-76459200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:76441800-76456800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:76441800-76458000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:76442000-76456800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:76442400-76455400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:76443000-76457600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr4:76443200-76456000	Weak transcription	Colonic Mucosa	Colon
28	chr4:76443200-76458800	Weak transcription	Stomach Mucosa	stomach
29	chr4:76443400-76470200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:76444400-76457400	Weak transcription	Hela-S3	cervix
31	chr4:76444400-76461000	Weak transcription	A549	lung
32	chr4:76444400-76471800	Weak transcription	Fetal Brain Male	brain
33	chr4:76445400-76455400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr4:76445400-76456400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:76445600-76456200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:76445600-76457600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:76445800-76458600	Strong transcription	Liver	Liver
38	chr4:76446200-76458200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:76446200-76458400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:76446200-76458400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:76446800-76456600	Strong transcription	Fetal Thymus	thymus
42	chr4:76446800-76458000	Strong transcription	Adipose Nuclei	Adipose
43	chr4:76447200-76455000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:76447200-76455800	Strong transcription	Dnd41	blood
45	chr4:76447200-76458200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr4:76447600-76457200	Strong transcription	Fetal Intestine Large	intestine
47	chr4:76447800-76456200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:76448400-76455400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:76448400-76456200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:76450000-76455200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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