Variant report

Variant	rs1887177
Chromosome Location	chr9:12771222-12771223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:12770939..12774696-chr9:12774747..12779041,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10115741	0.81[ASN][1000 genomes]
rs1041175	0.91[ASN][1000 genomes]
rs10733246	0.82[ASN][1000 genomes]
rs10733247	0.87[ASN][1000 genomes]
rs1074790	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs10756408	0.97[ASN][1000 genomes]
rs10809838	0.85[CEU][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10960780	0.89[ASN][1000 genomes]
rs10960786	0.93[ASN][1000 genomes]
rs1326779	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs1326781	0.82[ASN][1000 genomes]
rs1326794	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs1326796	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]
rs1409631	1.00[ASN][1000 genomes]
rs1409633	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs1887175	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[YRI][hapmap]
rs1887176	1.00[ASN][1000 genomes]
rs2147249	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs2181816	0.87[CHB][hapmap]
rs2209273	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[ASN][1000 genomes]
rs2209274	0.93[CHB][hapmap];0.93[ASN][1000 genomes]
rs2382362	0.82[ASN][1000 genomes]
rs2382363	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap]
rs2382364	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap]
rs2382368	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs4996096	0.87[ASN][1000 genomes]
rs7019486	0.80[CHD][hapmap]
rs7019981	0.80[CHD][hapmap]
rs7025099	0.95[ASN][1000 genomes]
rs7037828	0.96[ASN][1000 genomes]
rs7039957	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs7049095	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9696885	0.92[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	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	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
rs1887177	ZDHHC21	cis	parietal	SCAN
rs1887177	C9orf150	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12761200-12771800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:12761600-12774800	Weak transcription	NHLF	lung
3	chr9:12765400-12772000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:12766800-12771400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:12766800-12774800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:12766800-12774800	Weak transcription	HSMMtube	muscle
7	chr9:12767000-12771800	Weak transcription	A549	lung
8	chr9:12767200-12771800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:12768000-12771800	Weak transcription	Fetal Lung	lung
10	chr9:12770000-12771400	Enhancers	Fetal Intestine Large	intestine
11	chr9:12770400-12774800	Weak transcription	Fetal Intestine Small	intestine
12	chr9:12770600-12774800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:12771000-12772000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:12771000-12773000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links