Variant report

Variant	rs1817387
Chromosome Location	chr4:76446218-76446219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76439639..76442911-chr4:76442962..76447777,5	K562	blood:
2	chr4:76443470..76446392-chr4:76452432..76455084,2	K562	blood:
3	chr4:76438956..76440459-chr4:76445959..76447983,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163743	Chromatin interaction
ENSG00000174796	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10029348	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031553	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1046662	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11728327	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729929	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11730978	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735018	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13112378	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13145288	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1395359	0.96[CEU][hapmap]
rs1478174	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1580297	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1600100	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1841932	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1841934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045863	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2126855	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28507535	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867920	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867921	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59581284	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535523	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815241	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816603	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6823674	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6829753	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6833496	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841171	0.96[CEU][hapmap]
rs6841882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661659	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7664140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs786688	0.96[CEU][hapmap]
rs9041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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
rs1817387	THAP6	cis	multi-tissue	Pritchard
rs1817387	THAP6	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76440400-76448000	Weak transcription	Left Ventricle	heart
2	chr4:76440400-76450000	Weak transcription	Lung	lung
3	chr4:76440400-76453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:76440400-76454800	Weak transcription	Aorta	Aorta
5	chr4:76440400-76455200	Weak transcription	Esophagus	oesophagus
6	chr4:76440400-76456200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:76440400-76456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:76440400-76458000	Weak transcription	Spleen	Spleen
9	chr4:76440400-76458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:76440400-76466400	Weak transcription	Small Intestine	intestine
11	chr4:76440400-76473200	Weak transcription	Gastric	stomach
12	chr4:76440600-76451200	Weak transcription	Psoas Muscle	Psoas
13	chr4:76440600-76454800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:76440600-76455400	Weak transcription	Right Ventricle	heart
15	chr4:76440800-76448600	Weak transcription	Fetal Stomach	stomach
16	chr4:76440800-76450800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:76440800-76451000	Weak transcription	Brain Angular Gyrus	brain
18	chr4:76440800-76451000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:76440800-76454800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:76440800-76455800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:76440800-76455800	Weak transcription	Thymus	Thymus
22	chr4:76440800-76456000	Weak transcription	Pancreas	Pancrea
23	chr4:76440800-76457400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:76440800-76458600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:76441000-76451000	Weak transcription	Fetal Brain Female	brain
26	chr4:76441000-76454400	Weak transcription	HUVEC	blood vessel
27	chr4:76441000-76456400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:76441200-76452200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:76441400-76447800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:76441400-76448400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:76441400-76451000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:76441400-76456800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:76441400-76457400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:76441600-76447800	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:76441600-76450000	Weak transcription	NHEK	skin
36	chr4:76441600-76452600	Weak transcription	Fetal Heart	heart
37	chr4:76441600-76454000	Weak transcription	Fetal Intestine Small	intestine
38	chr4:76441600-76456400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:76441600-76457400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:76441600-76457600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:76441600-76458600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:76441600-76459200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:76441800-76448000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:76441800-76456800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:76441800-76458000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:76442000-76448800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:76442000-76456800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr4:76442400-76455400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:76442600-76448400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:76443000-76457600	Weak transcription	H9 Cell Line	embryonic stem cell

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