Variant report

Variant	rs9310073
Chromosome Location	chr3:88145028-88145029
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88143908..88145953-chr3:88197666..88200045,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163320	Chromatin interaction
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11128023	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1431154	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs1594453	1.00[EUR][1000 genomes]
rs1594455	1.00[EUR][1000 genomes]
rs1604700	1.00[EUR][1000 genomes]
rs1897238	1.00[EUR][1000 genomes]
rs2033390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2567037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2735557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241549	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4241550	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4287925	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303891	0.90[ASW][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs4404474	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4425287	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4443201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513473	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4515075	1.00[EUR][1000 genomes]
rs4616669	1.00[EUR][1000 genomes]
rs4858927	1.00[EUR][1000 genomes]
rs4858933	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858970	1.00[EUR][1000 genomes]
rs4858987	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4858988	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4858989	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6551270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621357	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625641	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633215	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7633486	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7636845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650749	1.00[EUR][1000 genomes]
rs7650912	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650915	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930154	1.00[EUR][1000 genomes]
rs9310062	1.00[EUR][1000 genomes]
rs9310063	1.00[EUR][1000 genomes]
rs9310069	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812903	1.00[EUR][1000 genomes]
rs9833231	1.00[EUR][1000 genomes]
rs9850550	1.00[EUR][1000 genomes]
rs9860113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9867614	1.00[EUR][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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9310073	ZNF654	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:88113200-88146200	Weak transcription	HMEC	breast
3	chr3:88125200-88163600	Weak transcription	NHDF-Ad	bronchial
4	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
5	chr3:88129600-88180200	Weak transcription	NHEK	skin
6	chr3:88129800-88151600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:88130600-88155000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:88132200-88147000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:88133800-88155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:88134000-88176400	Weak transcription	Ovary	ovary
11	chr3:88134200-88154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:88134200-88159400	Weak transcription	Fetal Heart	heart
13	chr3:88134800-88188200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:88135600-88196800	Weak transcription	Hela-S3	cervix
15	chr3:88136600-88148200	Weak transcription	Fetal Stomach	stomach
16	chr3:88137200-88155000	Weak transcription	Left Ventricle	heart
17	chr3:88137200-88162600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:88137400-88145200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:88137400-88155400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:88137400-88163800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:88137400-88188200	Weak transcription	Fetal Kidney	kidney
22	chr3:88138200-88146000	Weak transcription	Fetal Brain Female	brain
23	chr3:88138200-88180800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:88139200-88151800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:88139200-88163800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:88140200-88145400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:88140200-88163800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:88140400-88145400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:88140400-88146000	Weak transcription	Fetal Lung	lung
30	chr3:88140400-88146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:88140400-88154400	Weak transcription	Adipose Nuclei	Adipose
32	chr3:88140400-88163800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:88140400-88167000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:88140600-88163200	Weak transcription	Fetal Intestine Large	intestine
35	chr3:88140600-88163600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:88140800-88145200	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:88140800-88145600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:88140800-88145800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:88140800-88148000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:88140800-88150200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:88140800-88162600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:88140800-88162600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:88140800-88162600	Weak transcription	HSMM	muscle
44	chr3:88140800-88163200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:88140800-88163400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:88140800-88176000	Weak transcription	K562	blood
47	chr3:88141000-88145200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:88141000-88145800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:88141000-88163600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:88141000-88163800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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