Variant report

Variant	rs1326796
Chromosome Location	chr9:12774019-12774020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12770939..12774696-chr9:12774747..12779041,5	MCF-7	breast:
2	chr9:12771458..12774120-chr9:12775878..12777874,2	K562	blood:
3	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1041175	0.99[ASN][1000 genomes]
rs10733247	0.94[ASN][1000 genomes]
rs1074790	0.93[CHB][hapmap]
rs10756408	0.90[ASN][1000 genomes]
rs10809830	0.84[ASN][1000 genomes]
rs10809838	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10960780	0.84[ASN][1000 genomes]
rs10960786	1.00[ASN][1000 genomes]
rs1326794	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1409631	0.93[ASN][1000 genomes]
rs1409633	1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1854022	0.84[ASN][1000 genomes]
rs1887175	0.93[GIH][hapmap]
rs1887176	0.93[ASN][1000 genomes]
rs1887177	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2147249	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2181816	0.93[CHB][hapmap]
rs2209273	0.93[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs2209274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2382363	0.93[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2382364	0.93[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2382368	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs4996096	0.94[ASN][1000 genomes]
rs6474729	0.85[ASN][1000 genomes]
rs7019486	0.86[CHB][hapmap]
rs7019981	0.86[CHB][hapmap]
rs7025099	0.90[ASN][1000 genomes]
rs7037828	0.91[ASN][1000 genomes]
rs7039957	0.86[CHB][hapmap]
rs7049095	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9696885	0.85[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	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1326796	C9orf150	cis	parietal	SCAN
rs1326796	TXNDC9	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12761600-12774800	Weak transcription	NHLF	lung
2	chr9:12766800-12774800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:12766800-12774800	Weak transcription	HSMMtube	muscle
4	chr9:12770400-12774800	Weak transcription	Fetal Intestine Small	intestine
5	chr9:12770600-12774800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:12771400-12774800	Weak transcription	Fetal Intestine Large	intestine
7	chr9:12771800-12774600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:12772200-12774800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:12772400-12774800	Weak transcription	HUVEC	blood vessel
10	chr9:12772600-12774600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:12772600-12774600	Weak transcription	Osteobl	bone
12	chr9:12772600-12774800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:12772800-12774600	Weak transcription	A549	lung
14	chr9:12772800-12774600	Weak transcription	NH-A	brain
15	chr9:12772800-12774800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:12772800-12774800	Weak transcription	Hela-S3	cervix
17	chr9:12772800-12774800	Weak transcription	HSMM	muscle
18	chr9:12773000-12774800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:12773000-12774800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:12773000-12774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:12773000-12774800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:12773000-12774800	Weak transcription	Adipose Nuclei	Adipose
23	chr9:12773200-12774600	Weak transcription	NHDF-Ad	bronchial
24	chr9:12773200-12774800	Weak transcription	HMEC	breast
25	chr9:12773200-12774800	Weak transcription	NHEK	skin
26	chr9:12773400-12774600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:12773800-12774200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:12773800-12774200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:12773800-12774400	Enhancers	Liver	Liver
30	chr9:12774000-12774200	Flanking Active TSS	Fetal Lung	lung
31	chr9:12774000-12774800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links