Variant report

Variant	rs9640655
Chromosome Location	chr7:98017099-98017100
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	FOXA2	chr7:98017043-98017838	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:98015865..98017595-chr7:98028896..98031691,2	MCF-7	breast:

Variant related genes	Relation type
RPS3AP26	TF binding region
ENSG00000006453	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1006169	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10953254	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11768599	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11769950	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11772432	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533982	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12539761	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1541409	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985593	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240348	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3801258	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3944111	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236537	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729432	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55648546	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55946416	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56997921	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59120980	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62478160	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62478201	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62478228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62478235	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62479858	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9641236	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9641237	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9649213	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9640655	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97990400-98017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:97990400-98028000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:97992000-98029400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:97992800-98017400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:97995800-98028200	Weak transcription	Esophagus	oesophagus
6	chr7:98002600-98027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:98003000-98021600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:98003000-98023600	Weak transcription	Hela-S3	cervix
9	chr7:98004000-98017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:98005800-98018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:98007400-98028000	Weak transcription	Fetal Stomach	stomach
12	chr7:98007800-98018400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:98009800-98017800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:98010400-98021200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:98011200-98020800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:98011200-98021000	Weak transcription	GM12878-XiMat	blood
17	chr7:98011200-98021200	Weak transcription	HepG2	liver
18	chr7:98013600-98023600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:98014200-98027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:98014400-98017400	Weak transcription	Gastric	stomach
21	chr7:98014400-98017400	Weak transcription	Pancreas	Pancrea
22	chr7:98014600-98027400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:98014800-98018200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:98016200-98017400	Enhancers	Fetal Muscle Leg	muscle
25	chr7:98016200-98018000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:98016400-98017200	Enhancers	Fetal Muscle Trunk	muscle
27	chr7:98016400-98017200	Strong transcription	A549	lung
28	chr7:98016400-98017800	Enhancers	Duodenum Mucosa	Duodenum
29	chr7:98016400-98018200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr7:98016400-98018600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:98016400-98019200	Enhancers	Liver	Liver
32	chr7:98016600-98018000	Strong transcription	NHEK	skin
33	chr7:98016600-98018400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:98016600-98018600	Enhancers	Stomach Mucosa	stomach
35	chr7:98016800-98017600	Weak transcription	Colonic Mucosa	Colon
36	chr7:98016800-98018000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:98016800-98021200	Weak transcription	Fetal Intestine Small	intestine
38	chr7:98016800-98024000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:98016800-98027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:98017000-98017600	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links