Variant report

Variant	rs6949637
Chromosome Location	chr7:108094066-108094067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:108092926..108094617-chr7:108105069..108107356,2	K562	blood:
2	chr7:108093450..108095876-chr7:108096982..108099296,2	K562	blood:
3	chr7:107851104..107853420-chr7:108092854..108094489,2	MCF-7	breast:
4	chr7:108074243..108076743-chr7:108091855..108094696,3	MCF-7	breast:
5	chr7:107885138..107886888-chr7:108093240..108094894,2	K562	blood:
6	chr7:107831583..107833126-chr7:108092027..108094730,2	MCF-7	breast:
7	chr7:108087694..108090999-chr7:108091222..108094694,3	K562	blood:
8	chr7:108092671..108095154-chr7:108102924..108105484,2	MCF-7	breast:
9	chr7:108040975..108043949-chr7:108092664..108095074,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10487859	0.88[EUR][1000 genomes]
rs11971972	0.84[EUR][1000 genomes]
rs11973105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973823	0.83[EUR][1000 genomes]
rs11974559	0.85[EUR][1000 genomes]
rs11976021	0.84[EUR][1000 genomes]
rs11979596	0.84[EUR][1000 genomes]
rs11981670	0.88[EUR][1000 genomes]
rs11983900	0.81[EUR][1000 genomes]
rs12669879	0.84[EUR][1000 genomes]
rs12705470	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227836	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13228190	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13229488	0.88[EUR][1000 genomes]
rs13238841	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13245101	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245242	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13307045	0.86[EUR][1000 genomes]
rs13312593	0.86[EUR][1000 genomes]
rs17155828	0.87[EUR][1000 genomes]
rs17338441	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17338462	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17421351	0.84[EUR][1000 genomes]
rs17423043	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17423119	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17424206	0.88[EUR][1000 genomes]
rs194587	0.88[EUR][1000 genomes]
rs2108252	0.84[EUR][1000 genomes]
rs2108253	0.84[EUR][1000 genomes]
rs2214913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214914	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214915	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300040	0.81[EUR][1000 genomes]
rs2300048	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2300052	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395995	0.84[EUR][1000 genomes]
rs3202837	0.87[EUR][1000 genomes]
rs33987381	0.91[EUR][1000 genomes]
rs34218460	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34333829	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34583262	0.91[EUR][1000 genomes]
rs34814097	0.87[EUR][1000 genomes]
rs34887057	0.87[EUR][1000 genomes]
rs35429156	0.84[EUR][1000 genomes]
rs35436957	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35617326	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880371	0.83[EUR][1000 genomes]
rs40843	0.88[EUR][1000 genomes]
rs40845	0.88[EUR][1000 genomes]
rs40850	0.88[EUR][1000 genomes]
rs40854	0.85[EUR][1000 genomes]
rs40872	0.84[EUR][1000 genomes]
rs40875	0.86[EUR][1000 genomes]
rs40878	0.86[EUR][1000 genomes]
rs40880	0.83[EUR][1000 genomes]
rs40885	0.84[EUR][1000 genomes]
rs40886	0.83[EUR][1000 genomes]
rs40895	0.84[EUR][1000 genomes]
rs40899	0.84[EUR][1000 genomes]
rs40900	0.84[EUR][1000 genomes]
rs40901	0.84[EUR][1000 genomes]
rs40902	0.83[EUR][1000 genomes]
rs40908	0.84[EUR][1000 genomes]
rs40910	0.83[EUR][1000 genomes]
rs41385644	0.91[EUR][1000 genomes]
rs4992578	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56145857	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59458537	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60398019	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60426977	0.86[EUR][1000 genomes]
rs6466224	0.84[EUR][1000 genomes]
rs6466225	0.84[EUR][1000 genomes]
rs6466226	0.84[EUR][1000 genomes]
rs6466233	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6466238	0.85[EUR][1000 genomes]
rs66461825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67027479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67694466	0.86[EUR][1000 genomes]
rs6947492	0.87[EUR][1000 genomes]
rs6954366	0.84[EUR][1000 genomes]
rs6955152	0.88[EUR][1000 genomes]
rs6959023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959409	0.84[EUR][1000 genomes]
rs6960478	0.84[EUR][1000 genomes]
rs6966107	0.84[EUR][1000 genomes]
rs6967368	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969521	0.84[EUR][1000 genomes]
rs6976309	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976649	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976659	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976752	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976776	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976804	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71213282	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7786947	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790875	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7797885	0.84[EUR][1000 genomes]
rs7806869	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7807737	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807941	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811808	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9649307	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649308	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9785056	0.91[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6949637	THAP5	cis	Esophagus Muscularis	GTEx
rs6949637	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108076200-108094800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:108090000-108094600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr7:108090000-108095000	Weak transcription	Pancreas	Pancrea
4	chr7:108090200-108094200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr7:108090200-108094400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:108090200-108094600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:108090200-108094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:108090400-108094400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:108091000-108094600	Weak transcription	Brain Germinal Matrix	brain
10	chr7:108092200-108094600	Weak transcription	HSMMtube	muscle
11	chr7:108092800-108094600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:108092800-108094800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:108093000-108094400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:108093000-108095000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr7:108093000-108095000	Flanking Active TSS	A549	lung
16	chr7:108093000-108095200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:108093200-108094400	Enhancers	Brain Angular Gyrus	brain
18	chr7:108093200-108094600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:108093400-108094600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:108093600-108094400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:108093800-108094400	Enhancers	Fetal Brain Female	brain
22	chr7:108093800-108094600	Enhancers	Fetal Brain Male	brain
23	chr7:108093800-108094600	Enhancers	HMEC	breast
24	chr7:108093800-108095000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:108094000-108094400	Enhancers	HUVEC	blood vessel
26	chr7:108094000-108094600	Active TSS	Brain Cingulate Gyrus	brain
27	chr7:108094000-108094600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr7:108094000-108094800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:108094000-108095400	Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links