Variant report

Variant	rs7023577
Chromosome Location	chr9:96336993-96336994
allele	C/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	chr9:96336453-96336994	K562	blood:	n/a	n/a
2	POLR2A	chr9:96336879-96337049	MCF-7	breast:	n/a	n/a
3	POLR2A	chr9:96336738-96336996	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:96336738-96337162	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr9:96336945-96337049	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
2	chr9:96300899..96303747-chr9:96334511..96337154,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120AOS-5	chr9:96336376-96337293	NONHSAT133277

Variant related genes	Relation type
PHF2	TF binding region
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10115234	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10512225	0.82[MEX][hapmap]
rs10761234	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10761237	0.87[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10821126	0.82[AMR][1000 genomes]
rs10821131	0.85[AMR][1000 genomes]
rs10821135	0.81[ASW][hapmap];0.85[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes]
rs10821144	0.92[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821155	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10821162	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821166	0.81[CEU][hapmap]
rs10992783	0.94[ASN][1000 genomes]
rs10992788	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992789	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13292712	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3901421	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs3933795	0.91[MEX][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs4237221	0.92[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4310267	0.81[AMR][1000 genomes]
rs4607675	0.86[AMR][1000 genomes]
rs4743927	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744243	0.85[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs4744245	0.87[AMR][1000 genomes]
rs61707921	0.85[AMR][1000 genomes]
rs6479484	0.93[ASW][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes]
rs6479485	0.88[YRI][hapmap];0.90[AMR][1000 genomes]
rs6479492	0.92[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479493	0.92[CEU][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7019001	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7021689	0.86[AMR][1000 genomes]
rs7023212	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7035504	0.92[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040832	0.89[AMR][1000 genomes]
rs883782	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs883784	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs952288	0.92[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs966789	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7023577	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96330000-96337200	Weak transcription	NHLF	lung
2	chr9:96330000-96337400	Weak transcription	Hela-S3	cervix
3	chr9:96330000-96337400	Weak transcription	HSMM	muscle
4	chr9:96330200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:96330200-96337000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:96330200-96337000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:96330200-96337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:96330200-96337200	Weak transcription	Aorta	Aorta
9	chr9:96330200-96337200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:96330200-96337200	Weak transcription	Colonic Mucosa	Colon
11	chr9:96330200-96337200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:96330200-96337200	Weak transcription	Osteobl	bone
13	chr9:96330200-96337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:96330200-96337400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:96330200-96337400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:96330200-96337400	Weak transcription	Psoas Muscle	Psoas
17	chr9:96330200-96337400	Weak transcription	NHEK	skin
18	chr9:96330200-96337600	Weak transcription	Right Atrium	heart
19	chr9:96330400-96337000	Weak transcription	Fetal Heart	heart
20	chr9:96330800-96337200	Weak transcription	Pancreas	Pancrea
21	chr9:96331000-96337000	Weak transcription	Fetal Stomach	stomach
22	chr9:96332400-96337400	Weak transcription	Primary B cells from cord blood	blood
23	chr9:96332400-96337400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:96332600-96337400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:96333400-96337200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:96333400-96337200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:96333600-96337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:96333800-96337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:96333800-96337200	Weak transcription	Fetal Brain Female	brain
30	chr9:96333800-96337400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:96333800-96337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:96333800-96337600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:96334000-96337200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:96334000-96337400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:96334800-96337600	Enhancers	Fetal Thymus	thymus
36	chr9:96335400-96337000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:96335600-96337400	Weak transcription	Left Ventricle	heart
38	chr9:96335800-96337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:96335800-96337200	Enhancers	Placenta	Placenta
40	chr9:96336000-96337200	Weak transcription	Thymus	Thymus
41	chr9:96336400-96337000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:96336400-96337200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:96336400-96337200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:96336400-96337400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:96336400-96337400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr9:96336400-96337400	Enhancers	Brain Cingulate Gyrus	brain
47	chr9:96336400-96337400	Enhancers	Brain Hippocampus Middle	brain
48	chr9:96336400-96337400	Enhancers	Brain Substantia Nigra	brain
49	chr9:96336400-96337400	Enhancers	Fetal Muscle Leg	muscle
50	chr9:96336400-96337400	Enhancers	Monocytes-CD14+_RO01746	blood

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