Variant report

Variant	rs62478233
Chromosome Location	chr7:98023092-98023093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1076272	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10808107	0.92[EUR][1000 genomes]
rs10953255	0.83[EUR][1000 genomes]
rs10953256	0.92[EUR][1000 genomes]
rs10953257	0.93[EUR][1000 genomes]
rs10953261	0.84[ASN][1000 genomes]
rs1132971	0.83[EUR][1000 genomes]
rs11496115	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11760930	0.84[EUR][1000 genomes]
rs11761158	0.82[EUR][1000 genomes]
rs11761206	0.91[EUR][1000 genomes]
rs11765794	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11766808	0.84[EUR][1000 genomes]
rs12112351	0.89[EUR][1000 genomes]
rs12154723	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12667634	0.93[EUR][1000 genomes]
rs12671301	0.80[EUR][1000 genomes]
rs12672092	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12673586	0.88[EUR][1000 genomes]
rs12704982	0.84[EUR][1000 genomes]
rs12704983	0.82[EUR][1000 genomes]
rs12704988	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12704989	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12728	0.83[EUR][1000 genomes]
rs12873	0.83[EUR][1000 genomes]
rs13232181	0.89[EUR][1000 genomes]
rs13237102	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13238610	0.82[EUR][1000 genomes]
rs13245076	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13246725	0.84[EUR][1000 genomes]
rs13246843	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13246868	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13246942	0.84[EUR][1000 genomes]
rs13307593	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1468338	0.92[EUR][1000 genomes]
rs1468340	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1468341	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1859482	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2107716	0.90[EUR][1000 genomes]
rs2158553	0.91[EUR][1000 genomes]
rs2240349	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2286074	0.92[EUR][1000 genomes]
rs2394852	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2394854	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34129434	0.84[EUR][1000 genomes]
rs34534766	0.82[EUR][1000 genomes]
rs34695842	0.84[EUR][1000 genomes]
rs34717219	0.93[EUR][1000 genomes]
rs34835415	0.93[EUR][1000 genomes]
rs35535338	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35941058	0.84[EUR][1000 genomes]
rs35944487	0.81[EUR][1000 genomes]
rs35997266	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36017146	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36019673	0.85[EUR][1000 genomes]
rs36099592	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3779193	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779194	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801251	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801254	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801255	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801256	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801257	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801263	0.93[EUR][1000 genomes]
rs3801264	0.92[EUR][1000 genomes]
rs3823740	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4075057	0.84[EUR][1000 genomes]
rs55825602	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56286037	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60077733	0.91[EUR][1000 genomes]
rs62478174	0.88[EUR][1000 genomes]
rs62478175	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62478200	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62478203	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62478236	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62478237	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62479853	0.84[EUR][1000 genomes]
rs6465662	0.80[EUR][1000 genomes]
rs6465663	0.84[EUR][1000 genomes]
rs6465664	0.83[EUR][1000 genomes]
rs6465665	0.86[EUR][1000 genomes]
rs6465666	0.89[EUR][1000 genomes]
rs6465667	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6465669	0.90[EUR][1000 genomes]
rs6465670	0.90[EUR][1000 genomes]
rs6465671	0.92[EUR][1000 genomes]
rs6465672	0.93[EUR][1000 genomes]
rs6465673	0.90[EUR][1000 genomes]
rs6465675	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6465677	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465678	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465680	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6465681	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465682	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465683	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66548074	0.81[EUR][1000 genomes]
rs67132564	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944262	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6945554	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6947208	0.83[EUR][1000 genomes]
rs6947340	0.82[EUR][1000 genomes]
rs6948346	0.90[EUR][1000 genomes]
rs6948540	0.93[EUR][1000 genomes]
rs6949214	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6949718	0.84[EUR][1000 genomes]
rs6955647	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6956686	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6959506	0.93[EUR][1000 genomes]
rs6961129	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6961438	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6961790	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6963210	0.92[EUR][1000 genomes]
rs6967457	0.83[EUR][1000 genomes]
rs6967576	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6967934	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6968144	0.84[EUR][1000 genomes]
rs6968193	0.82[EUR][1000 genomes]
rs6968321	0.93[EUR][1000 genomes]
rs6969234	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6969731	0.84[EUR][1000 genomes]
rs6970801	0.84[EUR][1000 genomes]
rs6970990	0.84[EUR][1000 genomes]
rs6971825	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6973775	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6974943	0.93[EUR][1000 genomes]
rs6975156	0.83[EUR][1000 genomes]
rs6979373	0.93[EUR][1000 genomes]
rs71563562	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs73147342	0.84[EUR][1000 genomes]
rs736753	0.84[EUR][1000 genomes]
rs736754	0.84[EUR][1000 genomes]
rs7458551	0.92[EUR][1000 genomes]
rs7776638	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7777415	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7781916	0.84[EUR][1000 genomes]
rs7785612	0.82[EUR][1000 genomes]
rs7787009	0.81[ASN][1000 genomes]
rs7787418	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7787858	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7789380	0.92[EUR][1000 genomes]
rs7790229	0.83[EUR][1000 genomes]
rs7791321	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7794612	0.82[EUR][1000 genomes]
rs7795176	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7796611	0.82[EUR][1000 genomes]
rs7797943	0.92[EUR][1000 genomes]
rs7801992	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7802541	0.82[EUR][1000 genomes]
rs7802794	0.87[EUR][1000 genomes]
rs7803372	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7805267	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7806524	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7806739	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7807455	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7807555	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7812180	0.90[EUR][1000 genomes]
rs9648908	0.92[EUR][1000 genomes]
rs9769767	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv888766	chr7:97975542-98123880	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	nsv5860	chr7:97995939-98028100	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1795864	chr7:98013507-98040788	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv607919	chr7:98021211-98124854	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62478233	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs62478233	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97990400-98028000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:97992000-98029400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:97995800-98028200	Weak transcription	Esophagus	oesophagus
4	chr7:98002600-98027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:98003000-98023600	Weak transcription	Hela-S3	cervix
6	chr7:98007400-98028000	Weak transcription	Fetal Stomach	stomach
7	chr7:98013600-98023600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:98014200-98027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:98014600-98027400	Weak transcription	Fetal Intestine Large	intestine
10	chr7:98016800-98024000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:98016800-98027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:98017600-98023600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:98017600-98027800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:98017800-98028000	Weak transcription	Pancreas	Pancrea
15	chr7:98018000-98023600	Weak transcription	A549	lung
16	chr7:98018000-98027600	Weak transcription	NHEK	skin
17	chr7:98018000-98028000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:98018200-98024200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:98018600-98023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:98018600-98023800	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:98018600-98028000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:98018800-98028000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr7:98022000-98023600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:98022000-98023600	Weak transcription	Stomach Mucosa	stomach
25	chr7:98022000-98024000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:98022000-98027400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:98022000-98027400	Weak transcription	Fetal Intestine Small	intestine
28	chr7:98022000-98028000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:98022000-98029200	Weak transcription	Placenta	Placenta
30	chr7:98022200-98027200	Weak transcription	HepG2	liver
31	chr7:98022200-98027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:98022800-98025800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr7:98023000-98024400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links