Variant report

Variant	rs13317985
Chromosome Location	chr3:111456174-111456175
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111456141..111458585-chr3:111526075..111527610,2	MCF-7	breast:
2	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12632310	0.82[CEU][hapmap];0.82[MKK][hapmap]
rs13321524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13322494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs13325336	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17423838	1.00[ASW][hapmap];0.81[CEU][hapmap]
rs17489748	0.80[CEU][hapmap]
rs2292516	0.81[CEU][hapmap]
rs28479130	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28534728	0.93[EUR][1000 genomes]
rs28648833	0.93[EUR][1000 genomes]
rs28675079	0.83[EUR][1000 genomes]
rs3821919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3922706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3922780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4075549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4276156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4516581	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4542994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4634085	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4682313	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56052712	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56215064	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57902958	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58124137	0.93[EUR][1000 genomes]
rs58663746	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60867472	0.93[EUR][1000 genomes]
rs6438012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66651424	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66786213	0.93[EUR][1000 genomes]
rs66856712	0.93[EUR][1000 genomes]
rs66975684	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6762246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6762572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6778818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6782513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6787278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6789977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs6790355	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6790977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6795947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67970120	0.83[EUR][1000 genomes]
rs6798476	0.82[JPT][hapmap]
rs6800047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6800065	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6800922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6802960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs73220212	0.87[ASN][1000 genomes]
rs73222475	0.93[EUR][1000 genomes]
rs73222500	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7614433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627909	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs9842396	1.00[ASW][hapmap];1.00[CEU][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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9843288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9850748	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9858064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9858228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9862472	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9871034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9877777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9880633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs13317985	EMX1	trans	multi-tissue	Pritchard
rs13317985	LOC728684	cis	Liver	GTEx
rs13317985	IRAK1BP1	cis	Liver	GTEx
rs13317985	NOC4L	cis	Liver	GTEx
rs13317985	ADCK1	cis	Liver	GTEx
rs13317985	ARL4C	trans	multi-tissue	Pritchard
rs13317985	TMPRSS7	cis	parietal	SCAN
rs13317985	PFN4	cis	Liver	GTEx
rs13317985	hCT1829486.1	trans	multi-tissue	Pritchard
rs13317985	HMX3	trans	multi-tissue	Pritchard
rs13317985	C21orf110	cis	Liver	GTEx
rs13317985	EMX1	cis	Liver	GTEx
rs13317985	RSE_00000388885	trans	multi-tissue	Pritchard
rs13317985	TMPRSS7	cis	cerebellum	SCAN
rs13317985	AL137390	trans	multi-tissue	Pritchard
rs13317985	ARL4C	cis	Liver	GTEx
rs13317985	KDELC2	cis	Liver	GTEx
rs13317985	HMX3	cis	Liver	GTEx
rs13317985	NOC4L	trans	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:111452400-111458800	Enhancers	HMEC	breast
5	chr3:111452600-111457200	Enhancers	HSMM	muscle
6	chr3:111452800-111459200	Enhancers	Osteobl	bone
7	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
9	chr3:111453200-111456200	Weak transcription	Fetal Kidney	kidney
10	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
11	chr3:111453600-111456800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:111453600-111456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
16	chr3:111453800-111456600	Enhancers	NHLF	lung
17	chr3:111453800-111457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:111453800-111457600	Enhancers	NHEK	skin
19	chr3:111454200-111456800	Enhancers	NH-A	brain
20	chr3:111454200-111458200	Enhancers	Hela-S3	cervix
21	chr3:111454600-111458000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:111454600-111459400	Enhancers	HepG2	liver
23	chr3:111454600-111459600	Enhancers	Liver	Liver
24	chr3:111454800-111456200	Enhancers	A549	lung
25	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
26	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
27	chr3:111455000-111456600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:111455000-111457600	Weak transcription	HUVEC	blood vessel
29	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:111455200-111457000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:111455600-111456200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:111455600-111456400	Enhancers	Left Ventricle	heart
33	chr3:111455600-111456400	Enhancers	Ovary	ovary
34	chr3:111455600-111457000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:111455600-111458600	Enhancers	Right Atrium	heart
36	chr3:111455600-111458800	Enhancers	Adipose Nuclei	Adipose
37	chr3:111455800-111456200	Strong transcription	Primary T cells from cord blood	blood
38	chr3:111455800-111456200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:111455800-111456400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:111455800-111456400	Enhancers	Pancreas	Pancrea
41	chr3:111455800-111456400	Enhancers	Right Ventricle	heart
42	chr3:111455800-111457000	Enhancers	Small Intestine	intestine
43	chr3:111455800-111457200	Enhancers	Fetal Stomach	stomach
44	chr3:111455800-111458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:111455800-111458400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:111455800-111458600	Enhancers	Psoas Muscle	Psoas
47	chr3:111455800-111458800	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr3:111455800-111459000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:111455800-111459200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum

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