Variant report

Variant	rs10989072
Chromosome Location	chr9:103138400-103138401
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	chr9:103134684..103138813-chr9:103188908..103191193,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10819755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs10819757	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819760	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819765	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819766	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819768	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819771	0.91[CEU][hapmap]
rs10819772	0.91[CEU][hapmap]
rs10989041	0.90[EUR][1000 genomes]
rs10989046	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs10989047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989050	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989062	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989063	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989068	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989069	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989074	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10989077	1.00[ASN][1000 genomes]
rs11515449	0.89[EUR][1000 genomes]
rs11515542	0.89[EUR][1000 genomes]
rs11788648	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790431	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs11791637	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11791943	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793726	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794753	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11795004	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000794	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs12002124	0.91[CEU][hapmap];0.90[GIH][hapmap]
rs12003468	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs12005177	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352336	1.00[ASN][1000 genomes]
rs12375859	1.00[ASN][1000 genomes]
rs12379480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284601	0.81[GIH][hapmap]
rs16919024	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs3199998	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274951	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62579387	1.00[ASN][1000 genomes]
rs7028101	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036972	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037122	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037419	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039994	0.91[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs7849019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866700	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7873560	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874036	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103134400-103141800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:103134400-103152600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:103136400-103141600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:103137800-103138400	Enhancers	HepG2	liver
5	chr9:103137800-103138400	Enhancers	HMEC	breast
6	chr9:103137800-103138400	Enhancers	NHEK	skin
7	chr9:103138000-103138400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:103138000-103138400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:103138000-103138400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:103138000-103138400	Enhancers	Placenta	Placenta
11	chr9:103138000-103138400	Enhancers	K562	blood
12	chr9:103138200-103141200	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:103138200-103141400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:103138200-103141400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:103138400-103141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:103138400-103141600	Weak transcription	Placenta	Placenta
17	chr9:103138400-103141600	Weak transcription	HepG2	liver
18	chr9:103138400-103141600	Weak transcription	HMEC	breast
19	chr9:103138400-103141800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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