Variant report

Variant	rs1854709
Chromosome Location	chr9:6251455-6251456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6244528..6246233-chr9:6251156..6253683,2	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10115294	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10123132	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs10123605	0.92[EUR][1000 genomes]
rs10125053	0.85[CEU][hapmap]
rs10125090	0.85[CEU][hapmap]
rs10125313	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs1037885	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1048279	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491838	0.88[EUR][1000 genomes]
rs10739096	0.92[EUR][1000 genomes]
rs10739101	0.88[EUR][1000 genomes]
rs10739103	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10739104	0.88[EUR][1000 genomes]
rs10758756	0.87[AMR][1000 genomes]
rs10758762	0.88[EUR][1000 genomes]
rs10758763	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10758768	0.92[EUR][1000 genomes]
rs10815400	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815401	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10815429	0.84[EUR][1000 genomes]
rs10815430	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10975501	1.00[CEU][hapmap]
rs1156869	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs1322170	0.86[AMR][1000 genomes]
rs13293015	0.80[EUR][1000 genomes]
rs13293673	0.80[EUR][1000 genomes]
rs13298872	0.92[EUR][1000 genomes]
rs1330381	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1381038	0.88[EUR][1000 genomes]
rs1407357	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1407358	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1412420	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1855022	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2000198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2019737	0.88[EUR][1000 genomes]
rs2051003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2150964	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2150971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2381438	0.80[EUR][1000 genomes]
rs28615746	0.92[EUR][1000 genomes]
rs2890707	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs35301257	0.84[EUR][1000 genomes]
rs3847262	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3858051	0.88[EUR][1000 genomes]
rs4008347	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs424119	0.88[EUR][1000 genomes]
rs4475552	0.80[EUR][1000 genomes]
rs4742172	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4742177	0.88[EUR][1000 genomes]
rs4742180	0.92[EUR][1000 genomes]
rs4742198	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742200	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742203	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs503315	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs553048	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6477060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477067	0.88[EUR][1000 genomes]
rs67541153	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7020305	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7021445	0.92[EUR][1000 genomes]
rs7031407	0.92[EUR][1000 genomes]
rs7031967	0.88[EUR][1000 genomes]
rs7035574	0.84[EUR][1000 genomes]
rs7036990	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7039968	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7040374	0.84[EUR][1000 genomes]
rs7041863	0.85[CEU][hapmap]
rs7043824	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043887	0.92[EUR][1000 genomes]
rs7044749	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7045164	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs7048431	0.80[EUR][1000 genomes]
rs7350177	0.92[EUR][1000 genomes]
rs7851921	0.92[EUR][1000 genomes]
rs7852138	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7853322	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7858373	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7859139	0.88[EUR][1000 genomes]
rs7864212	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7873206	0.92[EUR][1000 genomes]
rs898673	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs922221	1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs980849	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs980850	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs993952	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv521598	chr9:6142157-6291125	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv892158	chr9:6149006-6266440	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1027270	chr9:6152434-6328227	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv539968	chr9:6152434-6328227	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
14	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active 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 miRNA target site	67 gene(s)	inside rSNPs	diseases
16	nsv1019912	chr9:6224906-6257395	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1854709	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6237200-6258400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:6238600-6252400	Weak transcription	Colon Smooth Muscle	Colon
3	chr9:6239400-6255200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:6239400-6257600	Weak transcription	Brain Anterior Caudate	brain
5	chr9:6239800-6251600	Weak transcription	Gastric	stomach
6	chr9:6243200-6255800	Weak transcription	Left Ventricle	heart
7	chr9:6243400-6256200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:6247600-6268800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:6248000-6258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:6249000-6253800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:6249200-6268000	Weak transcription	Fetal Stomach	stomach
12	chr9:6251000-6252800	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:6251000-6255600	Weak transcription	Fetal Brain Male	brain
14	chr9:6251400-6252400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:6251400-6253800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:6251400-6255000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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