Variant report

Variant	rs9648907
Chromosome Location	chr7:97945115-97945116
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	chr7:97943546..97945828-chr7:97977382..97980007,2	MCF-7	breast:
2	chr7:97944628..97945608-chr7:98424435..98424955,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10808107	0.83[EUR][1000 genomes]
rs10953256	0.83[EUR][1000 genomes]
rs10953257	0.83[EUR][1000 genomes]
rs11761206	0.81[EUR][1000 genomes]
rs11765794	0.83[EUR][1000 genomes]
rs12667634	0.83[EUR][1000 genomes]
rs12672092	0.83[EUR][1000 genomes]
rs12704988	0.80[EUR][1000 genomes]
rs13008	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13246843	0.82[EUR][1000 genomes]
rs13246868	0.83[EUR][1000 genomes]
rs13307593	0.83[EUR][1000 genomes]
rs1468338	0.83[EUR][1000 genomes]
rs1468340	0.83[EUR][1000 genomes]
rs1468341	0.83[EUR][1000 genomes]
rs1859482	0.83[EUR][1000 genomes]
rs2107716	0.80[EUR][1000 genomes]
rs2158553	0.82[EUR][1000 genomes]
rs2240349	0.83[EUR][1000 genomes]
rs2286074	0.83[EUR][1000 genomes]
rs2394852	0.80[EUR][1000 genomes]
rs34717219	0.83[EUR][1000 genomes]
rs34835415	0.83[EUR][1000 genomes]
rs35535338	0.83[EUR][1000 genomes]
rs35997266	0.83[EUR][1000 genomes]
rs36017146	0.83[EUR][1000 genomes]
rs36099592	0.82[EUR][1000 genomes]
rs3779194	0.82[EUR][1000 genomes]
rs3801254	0.82[EUR][1000 genomes]
rs3801255	0.82[EUR][1000 genomes]
rs3801256	0.83[EUR][1000 genomes]
rs3801257	0.83[EUR][1000 genomes]
rs3801263	0.83[EUR][1000 genomes]
rs3801264	0.83[EUR][1000 genomes]
rs3823740	0.83[EUR][1000 genomes]
rs55825602	0.81[EUR][1000 genomes]
rs60077733	0.83[EUR][1000 genomes]
rs62478175	0.80[EUR][1000 genomes]
rs62478200	0.83[EUR][1000 genomes]
rs6465667	0.83[EUR][1000 genomes]
rs6465671	0.82[EUR][1000 genomes]
rs6465672	0.83[EUR][1000 genomes]
rs6465673	0.80[EUR][1000 genomes]
rs6465675	0.83[EUR][1000 genomes]
rs6465677	0.82[EUR][1000 genomes]
rs6465678	0.82[EUR][1000 genomes]
rs6465680	0.82[EUR][1000 genomes]
rs6465682	0.80[EUR][1000 genomes]
rs67132564	0.81[EUR][1000 genomes]
rs6944262	0.83[EUR][1000 genomes]
rs6945554	0.82[EUR][1000 genomes]
rs6948540	0.82[EUR][1000 genomes]
rs6949214	0.83[EUR][1000 genomes]
rs6955647	0.82[EUR][1000 genomes]
rs6956686	0.82[EUR][1000 genomes]
rs6959506	0.83[EUR][1000 genomes]
rs6961129	0.83[EUR][1000 genomes]
rs6961438	0.82[EUR][1000 genomes]
rs6961790	0.82[EUR][1000 genomes]
rs6963210	0.83[EUR][1000 genomes]
rs6967576	0.80[EUR][1000 genomes]
rs6968321	0.83[EUR][1000 genomes]
rs6969234	0.83[EUR][1000 genomes]
rs6971825	0.83[EUR][1000 genomes]
rs6973775	0.82[EUR][1000 genomes]
rs6974943	0.83[EUR][1000 genomes]
rs6979373	0.83[EUR][1000 genomes]
rs7458551	0.83[EUR][1000 genomes]
rs7776638	0.82[EUR][1000 genomes]
rs7777415	0.83[EUR][1000 genomes]
rs7787418	0.83[EUR][1000 genomes]
rs7787858	0.82[EUR][1000 genomes]
rs7789380	0.83[EUR][1000 genomes]
rs7791321	0.80[EUR][1000 genomes]
rs7795176	0.83[EUR][1000 genomes]
rs7797943	0.83[EUR][1000 genomes]
rs7801992	0.83[EUR][1000 genomes]
rs7803372	0.83[EUR][1000 genomes]
rs7805267	0.81[EUR][1000 genomes]
rs7806739	0.82[EUR][1000 genomes]
rs7807455	0.82[EUR][1000 genomes]
rs7807555	0.83[EUR][1000 genomes]
rs7812180	1.00[ASW][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648908	0.82[EUR][1000 genomes]
rs9769767	0.82[EUR][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	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv1016826	chr7:97926133-97963717	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9648907	NPTX2	cis	parietal	SCAN
rs9648907	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs9648907	FIS1	cis	parietal	SCAN
rs9648907	TECPR1	cis	parietal	SCAN
rs9648907	ZNF394	cis	cerebellum	SCAN
rs9648907	GPC2	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97914200-97958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:97919200-97957600	Weak transcription	Right Atrium	heart
3	chr7:97922200-97946800	Weak transcription	Small Intestine	intestine
4	chr7:97923400-97952000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:97924600-97952200	Weak transcription	Fetal Kidney	kidney
6	chr7:97924600-97952800	Weak transcription	NH-A	brain
7	chr7:97927600-97948200	Weak transcription	Brain Germinal Matrix	brain
8	chr7:97928800-97947400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr7:97929400-97945200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr7:97929400-97945800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr7:97929400-97947400	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr7:97933000-97948400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:97933600-97952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:97933800-97947000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:97934800-97947400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:97935200-97946000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:97935800-97951800	Weak transcription	Right Ventricle	heart
18	chr7:97935800-97968600	Weak transcription	Hela-S3	cervix
19	chr7:97937400-97946800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:97937600-97952200	Weak transcription	NHLF	lung
21	chr7:97937800-97946600	Weak transcription	Ovary	ovary
22	chr7:97937800-97946800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:97937800-97948200	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:97937800-97950600	Weak transcription	Spleen	Spleen
25	chr7:97937800-97951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:97938000-97946600	Weak transcription	Aorta	Aorta
27	chr7:97938200-97951000	Weak transcription	Left Ventricle	heart
28	chr7:97938800-97945200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:97939000-97948800	Strong transcription	A549	lung
30	chr7:97939200-97946600	Weak transcription	Pancreas	Pancrea
31	chr7:97939200-97948600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:97939200-97948600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:97939200-97951800	Weak transcription	Osteobl	bone
34	chr7:97939600-97946800	Weak transcription	Stomach Mucosa	stomach
35	chr7:97940400-97946800	Weak transcription	Colonic Mucosa	Colon
36	chr7:97940600-97945200	Strong transcription	Fetal Stomach	stomach
37	chr7:97942000-97950200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr7:97942200-97946800	Weak transcription	Lung	lung
39	chr7:97942600-97945400	Enhancers	Primary B cells from cord blood	blood
40	chr7:97942600-97945600	Genic enhancers	GM12878-XiMat	blood
41	chr7:97942600-97950600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:97942800-97946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:97943000-97947400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:97943000-97952200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:97943200-97946800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:97943200-97949400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:97943600-97945200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:97943600-97945200	Strong transcription	HMEC	breast
49	chr7:97943600-97946400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:97943600-97949400	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links