Variant report

Variant	rs2675168
Chromosome Location	chr9:97487605-97487606
allele	A/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	GATA3	chr9:97487429-97487610	SH-SY5Y	brain:	n/a	chr9:97487445-97487453 chr9:97487436-97487444

No.	Distal block	Cell Line	Cell type
1	chr9:97487422..97488922-chr9:97489538..97492187,2	K562	blood:
2	chr9:97476575..97480108-chr9:97483463..97488738,5	MCF-7	breast:
3	chr9:97483583..97486374-chr9:97487367..97488932,2	K562	blood:
4	chr9:97399286..97401961-chr9:97487355..97490023,2	MCF-7	breast:
5	chr9:97484874..97487089-chr9:97487277..97488932,2	K562	blood:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000165140	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10733756	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10761360	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10761363	0.92[AFR][1000 genomes]
rs10821407	0.80[AMR][1000 genomes]
rs12553916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382411	0.95[AFR][1000 genomes]
rs1382412	0.95[AFR][1000 genomes]
rs1530331	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1542108	0.92[AFR][1000 genomes]
rs16911856	0.87[AFR][1000 genomes]
rs17355875	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2099868	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2165715	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs242260	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2584805	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356125	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356128	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356132	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356133	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356136	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs356139	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356145	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356147	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356148	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs365465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs367319	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3887267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3910730	0.92[AFR][1000 genomes]
rs397783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316526	0.95[AFR][1000 genomes]
rs422502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs448899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs456276	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs457795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4612413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743968	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743970	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4743972	0.92[AFR][1000 genomes]
rs4743973	0.92[AFR][1000 genomes]
rs4744382	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744387	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4744388	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4744402	0.84[AFR][1000 genomes]
rs555799	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56198429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562605	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56317174	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56965843	0.80[EUR][1000 genomes]
rs58281499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60553517	0.82[AFR][1000 genomes]
rs61086657	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479569	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479575	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6479576	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6479577	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479579	0.83[AFR][1000 genomes]
rs6479582	0.92[AFR][1000 genomes]
rs6479583	0.92[AFR][1000 genomes]
rs66495734	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66642068	0.95[AFR][1000 genomes]
rs66710673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66863985	0.95[AFR][1000 genomes]
rs67208365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68090960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68091393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025934	0.81[EUR][1000 genomes]
rs7026714	0.80[AMR][1000 genomes]
rs7035166	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7037239	0.82[AFR][1000 genomes]
rs7038519	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7038891	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7047478	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72747019	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341710	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73532323	0.82[AFR][1000 genomes]
rs73532332	0.82[AFR][1000 genomes]
rs73532340	0.82[AFR][1000 genomes]
rs73532355	0.82[AFR][1000 genomes]
rs73534109	0.82[AFR][1000 genomes]
rs73534113	0.82[AFR][1000 genomes]
rs73534154	0.82[AFR][1000 genomes]
rs73534159	0.82[AFR][1000 genomes]
rs73536042	0.82[AFR][1000 genomes]
rs73536067	0.82[AFR][1000 genomes]
rs73536074	0.82[AFR][1000 genomes]
rs73538140	0.82[AFR][1000 genomes]
rs73538152	0.82[AFR][1000 genomes]
rs73538177	0.95[AFR][1000 genomes]
rs73540059	0.82[AFR][1000 genomes]
rs73540062	0.82[AFR][1000 genomes]
rs7855781	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7870679	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs894428	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9409589	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9409805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97479000-97488400	Weak transcription	Fetal Intestine Large	intestine
2	chr9:97483400-97488200	Weak transcription	Placenta	Placenta
3	chr9:97483600-97488400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:97483600-97488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:97483600-97488600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:97483800-97488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:97483800-97488400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:97483800-97488400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:97483800-97488400	Weak transcription	NHEK	skin
10	chr9:97484000-97488400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:97484000-97488400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:97484200-97488400	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:97484400-97488400	Weak transcription	Fetal Kidney	kidney
14	chr9:97484800-97488600	Weak transcription	NHDF-Ad	bronchial
15	chr9:97486600-97487800	Enhancers	Osteobl	bone
16	chr9:97486600-97488400	Enhancers	HepG2	liver
17	chr9:97487400-97488400	Weak transcription	Hela-S3	cervix
18	chr9:97487400-97488400	Weak transcription	K562	blood
19	chr9:97487400-97488400	Weak transcription	NH-A	brain
20	chr9:97487600-97487800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:97487600-97490000	Active TSS	Rectal Mucosa Donor 29	rectum

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