Variant report

Variant	rs34509359
Chromosome Location	chr9:12694255-12694256
allele	G/T
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	POLR2A	chr9:12694205-12694307	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf150-4	chr9:12693912-12694487	NONHSAT130224

Variant related genes	Relation type
TYRP1	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10960766	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10960767	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10960768	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11787674	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11787999	1.00[EUR][1000 genomes]
rs11788192	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11789339	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11789481	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11789805	0.90[EUR][1000 genomes]
rs11791137	1.00[AFR][1000 genomes]
rs11791392	1.00[AFR][1000 genomes]
rs11791497	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11791954	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11793178	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11793280	1.00[AFR][1000 genomes]
rs11794050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11794202	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11795082	1.00[AFR][1000 genomes]
rs12001299	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12001737	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12001745	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12001885	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12001964	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12005881	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929383	1.00[EUR][1000 genomes]
rs16929385	1.00[EUR][1000 genomes]
rs16929391	1.00[EUR][1000 genomes]
rs16929400	0.98[EUR][1000 genomes]
rs16929473	0.83[EUR][1000 genomes]
rs17280279	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17280629	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17346748	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2209278	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35238630	0.90[EUR][1000 genomes]
rs35852762	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35866166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3891858	0.98[EUR][1000 genomes]
rs41306290	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41314571	1.00[AFR][1000 genomes]
rs58067523	0.81[EUR][1000 genomes]
rs61758391	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61758394	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62638049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7025241	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7025758	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7026121	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7026199	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7030751	0.93[EUR][1000 genomes]
rs7033962	0.93[EUR][1000 genomes]
rs7035710	0.88[EUR][1000 genomes]
rs7040346	1.00[EUR][1000 genomes]
rs7041590	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7041735	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73402088	0.83[EUR][1000 genomes]
rs73402092	0.83[EUR][1000 genomes]
rs768617	1.00[EUR][1000 genomes]
rs7875424	1.00[EUR][1000 genomes]
rs7876041	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027260	chr9:12196141-12709959	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv540062	chr9:12196141-12709959	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv831513	chr9:12531673-12695747	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv892572	chr9:12549675-12715816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1016570	chr9:12576095-12722387	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	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
14	nsv466255	chr9:12628213-12699776	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv613611	chr9:12628213-12699776	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv466256	chr9:12628213-12712157	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv613612	chr9:12628213-12712157	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	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

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12690400-12695600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:12690400-12695600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:12693000-12710000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:12694000-12694400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:12694000-12699400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin

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