Variant report

Variant	rs10953258
Chromosome Location	chr7:97972639-97972640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4506131	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4727392	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951286	0.86[EUR][1000 genomes];0.84[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10953258	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97944800-97983400	Weak transcription	HepG2	liver
2	chr7:97953200-97978000	Weak transcription	Lung	lung
3	chr7:97953200-97978200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:97953800-97989800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:97954000-97980400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:97954400-97983800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:97958800-97981400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:97960200-97978400	Weak transcription	Fetal Stomach	stomach
9	chr7:97965400-97972800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:97966800-97983800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:97968000-97982000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:97968200-97978200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:97968400-97983600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr7:97969200-97973000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:97969200-97978000	Weak transcription	Gastric	stomach
16	chr7:97969200-97978000	Weak transcription	Hela-S3	cervix
17	chr7:97969200-97980600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:97969200-97981400	Weak transcription	Fetal Intestine Large	intestine
19	chr7:97969200-97981800	Weak transcription	Colonic Mucosa	Colon
20	chr7:97969400-97975800	Weak transcription	GM12878-XiMat	blood
21	chr7:97969400-97978000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:97969400-97978000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:97969400-97978000	Weak transcription	Esophagus	oesophagus
24	chr7:97969400-97978000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:97969400-97978000	Weak transcription	NHEK	skin
26	chr7:97969400-97979200	Weak transcription	HMEC	breast
27	chr7:97970200-97972800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:97971000-97975800	Weak transcription	A549	lung
29	chr7:97971000-97976000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:97971000-97976000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:97971200-97975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:97971200-97981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:97971200-97981600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:97971200-97981600	Weak transcription	Osteobl	bone
35	chr7:97971600-97973400	Enhancers	Stomach Mucosa	stomach
36	chr7:97972400-97972800	Weak transcription	Liver	Liver
37	chr7:97972400-97973000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:97972400-97979800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:97972400-97983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:97972600-97973000	Weak transcription	Pancreas	Pancrea
41	chr7:97972600-97973200	Enhancers	Fetal Intestine Small	intestine

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