Variant report

Variant	rs4974489
Chromosome Location	chr3:134053382-134053383
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134052272..134054008-chr3:134054064..134057061,2	K562	blood:
2	chr3:134052518..134054585-chr3:134071720..134074558,2	K562	blood:
3	chr3:134048500..134051081-chr3:134051265..134053947,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10755085	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs1111516	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11708815	0.86[ASN][1000 genomes]
rs11719057	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495847	0.80[ASN][1000 genomes]
rs13075185	0.86[ASN][1000 genomes]
rs13322269	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs1353776	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1353777	0.80[ASN][1000 genomes]
rs1353778	0.89[CHB][hapmap]
rs1466827	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1498731	0.95[ASN][1000 genomes]
rs1603824	0.95[ASN][1000 genomes]
rs1863910	0.80[ASN][1000 genomes]
rs2133307	0.95[ASN][1000 genomes]
rs2400278	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400279	0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2400280	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34341902	0.95[ASN][1000 genomes]
rs35951257	0.95[ASN][1000 genomes]
rs3732852	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773820	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3821705	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4264700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974485	0.95[ASN][1000 genomes]
rs4974486	1.00[JPT][hapmap]
rs4974487	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974491	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974494	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974495	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974496	0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4974497	0.95[ASN][1000 genomes]
rs4974498	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6439477	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6439478	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6786148	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613066	0.86[ASN][1000 genomes]
rs9450	0.95[ASN][1000 genomes]
rs9817900	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853621	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4974489	STAG1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134035000-134058800	Weak transcription	Liver	Liver
2	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:134042000-134060800	Enhancers	Placenta	Placenta
4	chr3:134042600-134054000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:134042600-134054400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:134044000-134054400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:134045000-134056400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:134046600-134053600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:134047400-134054000	Enhancers	NH-A	brain
11	chr3:134047600-134054200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:134048400-134054000	Enhancers	Aorta	Aorta
13	chr3:134048600-134053800	Weak transcription	HUVEC	blood vessel
14	chr3:134048600-134054200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:134049000-134054200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:134049000-134054200	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:134049000-134054600	Enhancers	Fetal Muscle Leg	muscle
18	chr3:134049200-134060800	Enhancers	Fetal Intestine Large	intestine
19	chr3:134049400-134054200	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:134049600-134054400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:134049600-134054400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:134049600-134054600	Enhancers	Fetal Stomach	stomach
23	chr3:134049600-134054600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr3:134049600-134054800	Enhancers	Lung	lung
25	chr3:134049800-134053600	Enhancers	Fetal Muscle Trunk	muscle
26	chr3:134049800-134054200	Enhancers	Ovary	ovary
27	chr3:134049800-134054400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr3:134050200-134054400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:134050600-134056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:134050600-134057000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:134050600-134060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:134050800-134054000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:134050800-134054200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:134050800-134054800	Enhancers	Colon Smooth Muscle	Colon
35	chr3:134050800-134061000	Weak transcription	Fetal Brain Female	brain
36	chr3:134051000-134053600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:134051000-134054200	Enhancers	HSMM	muscle
38	chr3:134051000-134055800	Enhancers	NHLF	lung
39	chr3:134051000-134056000	Enhancers	NHDF-Ad	bronchial
40	chr3:134051000-134056800	Enhancers	Osteobl	bone
41	chr3:134051200-134054200	Enhancers	HMEC	breast
42	chr3:134051200-134054800	Enhancers	HSMMtube	muscle
43	chr3:134051200-134056600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:134051400-134054000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:134051400-134054200	Enhancers	NHEK	skin
46	chr3:134051400-134054600	Enhancers	A549	lung
47	chr3:134051400-134055200	Enhancers	Hela-S3	cervix
48	chr3:134051400-134056200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:134051400-134056200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr3:134051400-134058800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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