Variant report

Variant	rs10756406
Chromosome Location	chr9:12748587-12748588
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	chr9:12748565..12752577-chr9:12774636..12778893,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10123986	0.82[AFR][1000 genomes]
rs10124197	0.83[AFR][1000 genomes]
rs10491742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10491743	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10491744	1.00[ASN][1000 genomes]
rs1063380	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1074789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074790	0.84[ASW][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs10756405	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10809826	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs10809836	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10960759	1.00[ASN][1000 genomes]
rs10960760	1.00[ASN][1000 genomes]
rs10960762	1.00[CHB][hapmap]
rs10960764	1.00[ASN][1000 genomes]
rs10960774	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10960775	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10960779	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10960781	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1134311	1.00[ASN][1000 genomes]
rs1137134	1.00[ASN][1000 genomes]
rs11789751	1.00[ASN][1000 genomes]
rs11829	1.00[ASN][1000 genomes]
rs12115198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379024	1.00[ASN][1000 genomes]
rs12379260	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs12552462	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1326788	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1326789	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1326790	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1326791	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1326792	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1326797	1.00[ASN][1000 genomes]
rs1326798	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs13284453	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13284898	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs13288130	1.00[ASN][1000 genomes]
rs13288475	1.00[ASN][1000 genomes]
rs13288636	1.00[ASN][1000 genomes]
rs13288681	1.00[ASN][1000 genomes]
rs13289304	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13302551	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1409626	1.00[ASN][1000 genomes]
rs1409629	0.89[ASN][1000 genomes]
rs1409630	0.89[ASN][1000 genomes]
rs1543587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17346161	1.00[CHB][hapmap]
rs2209269	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2209271	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2209277	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2224863	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2382361	1.00[ASN][1000 genomes]
rs2733830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733831	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733832	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733833	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2733834	1.00[CHB][hapmap]
rs2733836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2762458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2762460	0.86[CEU][hapmap]
rs2762461	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2762463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2762464	1.00[CHB][hapmap]
rs2890965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35666741	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4741245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683	1.00[CHB][hapmap]
rs7019486	0.83[YRI][hapmap]
rs7019981	0.83[YRI][hapmap]
rs7021368	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7023927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7025678	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7025771	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7025812	1.00[ASN][1000 genomes]
rs7025842	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7025914	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7025953	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7028587	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7030485	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7035500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7036011	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7039325	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7044022	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7466623	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs910	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs927868	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927869	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958073	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][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	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	esv2757318	chr9:12721881-12758881	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv8420	chr9:12725200-12750151	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3693020	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv818690	chr9:12726962-12748962	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	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
16	nsv518878	chr9:12748486-12748633	Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10756406	C9orf150	cis	intralobular white matter	BrainEAC
rs10756406	C9orf150	cis	parietal	SCAN
rs10756406	C9orf150	cis	brain	BrainEAC

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12747600-12748600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr9:12747600-12748800	Enhancers	NHDF-Ad	bronchial
3	chr9:12747600-12749200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:12747800-12748600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:12747800-12748600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:12748000-12748600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:12748000-12748800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:12748200-12748600	Enhancers	Hela-S3	cervix
9	chr9:12748200-12748600	Enhancers	HMEC	breast
10	chr9:12748200-12748800	Enhancers	NHEK	skin
11	chr9:12748200-12749200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:12748400-12749400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:12748400-12749400	Enhancers	Rectal Mucosa Donor 31	rectum

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