Variant report

Variant	rs28507535
Chromosome Location	chr4:76435772-76435773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:76435663-76435788	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:76422807..76425261-chr4:76435739..76438350,2	MCF-7	breast:
2	chr4:76433807..76436085-chr4:76437020..76439277,2	MCF-7	breast:
3	chr4:76435271..76437331-chr4:76452184..76454371,2	K562	blood:
4	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:

Variant related genes	Relation type
RCHY1	TF binding region
THAP6	TF binding region
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	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031553	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046662	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729929	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735018	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145288	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478174	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580297	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1817387	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1841932	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045863	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126855	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867920	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867921	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59581284	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535523	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815241	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816603	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823674	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829753	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833496	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841882	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661659	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664140	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9041	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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
rs28507535	THAP6	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
2	chr4:76395800-76437000	Weak transcription	Lung	lung
3	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
4	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
5	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
8	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
9	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
12	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:76415400-76436400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:76416600-76436200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:76416600-76437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:76417600-76436800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:76421400-76437000	Weak transcription	Stomach Mucosa	stomach
18	chr4:76424800-76436200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:76424800-76437000	Weak transcription	Psoas Muscle	Psoas
20	chr4:76424800-76437000	Weak transcription	NHLF	lung
21	chr4:76425000-76437000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:76425400-76437000	Weak transcription	Right Ventricle	heart
24	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:76425600-76436600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:76426000-76436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:76427000-76435800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:76427800-76437200	Weak transcription	Fetal Stomach	stomach
29	chr4:76428400-76437400	Weak transcription	A549	lung
30	chr4:76428600-76436600	Weak transcription	Brain Germinal Matrix	brain
31	chr4:76429000-76437000	Weak transcription	Fetal Intestine Small	intestine
32	chr4:76430400-76437000	Weak transcription	HSMMtube	muscle
33	chr4:76430600-76436200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:76430600-76436600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:76430600-76436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:76430600-76437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:76430600-76437000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:76430600-76437000	Weak transcription	Thymus	Thymus
39	chr4:76430800-76436800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:76430800-76437200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:76430800-76438200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:76431000-76436800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:76431000-76437000	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:76431200-76436600	Weak transcription	Fetal Brain Female	brain
45	chr4:76431200-76436800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:76431200-76437200	Weak transcription	Colonic Mucosa	Colon
47	chr4:76431400-76435800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:76431400-76436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:76431400-76436200	Weak transcription	Fetal Intestine Large	intestine
50	chr4:76431400-76437000	Weak transcription	NH-A	brain

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