Variant report

Variant	rs13246043
Chromosome Location	chr7:97998978-97998979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97998858..98000704-chr7:98027178..98028821,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10808107	0.82[ASN][1000 genomes]
rs10953256	0.82[ASN][1000 genomes]
rs10953257	0.86[ASN][1000 genomes]
rs11761206	0.81[ASN][1000 genomes]
rs11765794	0.86[ASN][1000 genomes]
rs12112351	0.82[ASN][1000 genomes]
rs12667634	0.86[ASN][1000 genomes]
rs12672092	0.84[ASN][1000 genomes]
rs12673586	0.82[ASN][1000 genomes]
rs12704988	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13232181	0.82[ASN][1000 genomes]
rs13245076	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13246843	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13246868	0.90[ASN][1000 genomes]
rs13307593	0.88[ASN][1000 genomes]
rs1468338	0.82[ASN][1000 genomes]
rs1468340	0.90[ASN][1000 genomes]
rs1468341	0.86[ASN][1000 genomes]
rs1859482	0.88[ASN][1000 genomes]
rs2107716	0.82[ASN][1000 genomes]
rs2158553	0.82[ASN][1000 genomes]
rs2240349	0.88[ASN][1000 genomes]
rs2286074	0.81[ASN][1000 genomes]
rs2394852	0.82[ASN][1000 genomes]
rs34717219	0.86[ASN][1000 genomes]
rs34835415	0.86[ASN][1000 genomes]
rs35535338	0.86[ASN][1000 genomes]
rs35997266	0.86[ASN][1000 genomes]
rs36017146	0.86[ASN][1000 genomes]
rs36099592	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3779194	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3801254	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3801255	0.91[ASN][1000 genomes]
rs3801256	0.91[ASN][1000 genomes]
rs3801257	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3801263	0.86[ASN][1000 genomes]
rs3801264	0.82[ASN][1000 genomes]
rs3823740	0.84[ASN][1000 genomes]
rs55825602	0.83[ASN][1000 genomes]
rs56286037	0.81[ASN][1000 genomes]
rs62478174	0.84[ASN][1000 genomes]
rs62478175	0.83[ASN][1000 genomes]
rs62478200	0.85[ASN][1000 genomes]
rs62478203	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6465666	0.82[ASN][1000 genomes]
rs6465667	0.84[ASN][1000 genomes]
rs6465669	0.86[ASN][1000 genomes]
rs6465670	0.86[ASN][1000 genomes]
rs6465671	0.83[ASN][1000 genomes]
rs6465672	0.86[ASN][1000 genomes]
rs6465673	0.84[ASN][1000 genomes]
rs6465675	0.86[ASN][1000 genomes]
rs6465677	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6465678	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6465680	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6465681	0.81[ASN][1000 genomes]
rs6465682	0.81[ASN][1000 genomes]
rs67132564	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6944262	0.88[ASN][1000 genomes]
rs6945554	0.86[ASN][1000 genomes]
rs6948346	0.86[ASN][1000 genomes]
rs6948540	0.86[ASN][1000 genomes]
rs6949214	0.86[ASN][1000 genomes]
rs6955647	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6956686	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6959506	0.85[ASN][1000 genomes]
rs6961129	0.86[ASN][1000 genomes]
rs6961438	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6961790	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6963210	0.82[ASN][1000 genomes]
rs6967576	0.81[ASN][1000 genomes]
rs6967934	0.86[ASN][1000 genomes]
rs6968321	0.86[ASN][1000 genomes]
rs6969234	0.90[ASN][1000 genomes]
rs6971825	0.86[ASN][1000 genomes]
rs6973775	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6974943	0.86[ASN][1000 genomes]
rs6979373	0.86[ASN][1000 genomes]
rs71563562	0.85[ASN][1000 genomes]
rs7458551	0.82[ASN][1000 genomes]
rs7776638	0.91[ASN][1000 genomes]
rs7777415	0.84[ASN][1000 genomes]
rs7786789	0.81[ASN][1000 genomes]
rs7787418	0.84[ASN][1000 genomes]
rs7787858	0.85[ASN][1000 genomes]
rs7789380	0.82[ASN][1000 genomes]
rs7791321	0.82[ASN][1000 genomes]
rs7795176	0.86[ASN][1000 genomes]
rs7797943	0.82[ASN][1000 genomes]
rs7801992	0.86[ASN][1000 genomes]
rs7803372	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7805267	0.84[ASN][1000 genomes]
rs7806524	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7806739	0.85[ASN][1000 genomes]
rs7807455	0.84[ASN][1000 genomes]
rs7807555	0.84[ASN][1000 genomes]
rs9648908	0.82[ASN][1000 genomes]
rs9769767	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13246043	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97977200-98010200	Weak transcription	GM12878-XiMat	blood
2	chr7:97984800-98000200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:97984800-98002200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:97990400-98017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:97990400-98028000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:97990600-98010400	Weak transcription	HepG2	liver
7	chr7:97991000-97999200	Weak transcription	Hela-S3	cervix
8	chr7:97991000-98002200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr7:97992000-98000200	Weak transcription	HMEC	breast
10	chr7:97992000-98029400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:97992200-97999200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:97992800-98017400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:97993800-98005400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:97994600-98000600	Enhancers	Stomach Mucosa	stomach
15	chr7:97995600-97999400	Weak transcription	Osteobl	bone
16	chr7:97995600-98002400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:97995600-98002400	Weak transcription	NH-A	brain
18	chr7:97995800-98000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:97995800-98000200	Weak transcription	Pancreas	Pancrea
20	chr7:97995800-98028200	Weak transcription	Esophagus	oesophagus
21	chr7:97996000-98000200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:97996200-97999200	Weak transcription	Adipose Nuclei	Adipose
23	chr7:97996200-97999400	Weak transcription	Lung	lung
24	chr7:97996200-98000200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:97996200-98001000	Weak transcription	Placenta	Placenta
26	chr7:97996200-98002800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:97996400-97999000	Weak transcription	Fetal Intestine Small	intestine
28	chr7:97996800-98000200	Weak transcription	NHEK	skin
29	chr7:97998000-97999400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:97998200-97999400	Enhancers	HUVEC	blood vessel
31	chr7:97998200-97999600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr7:97998200-98003200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr7:97998600-97999200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:97998600-97999200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:97998600-98000200	Weak transcription	A549	lung
36	chr7:97998600-98001000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:97998800-98002000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:97998800-98002000	Weak transcription	Fetal Muscle Leg	muscle
39	chr7:97998800-98008000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links