Variant report

Variant	rs323879
Chromosome Location	chr3:51984914-51984915
allele	A/G
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	TEAD4	chr3:51984874-51985365	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51984016..51985796-chr3:51991262..51993294,2	MCF-7	breast:
2	chr3:51975203..51979245-chr3:51981875..51985291,4	K562	blood:
3	chr3:51983749..51985969-chr3:52006072..52007842,2	K562	blood:

Variant related genes	Relation type
GPR62	TF binding region
ENSG00000114767	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11916396	0.90[AMR][1000 genomes]
rs11926611	1.00[CEU][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1876052	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2015691	1.00[MEX][hapmap];0.81[MKK][hapmap]
rs2271069	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323858	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs323861	0.90[AMR][1000 genomes]
rs323862	0.90[AMR][1000 genomes]
rs323863	1.00[MEX][hapmap]
rs323864	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs323865	0.81[ASW][hapmap];0.82[LWK][hapmap];0.83[AFR][1000 genomes]
rs323866	0.83[AFR][1000 genomes]
rs323867	0.81[ASW][hapmap];0.83[AFR][1000 genomes]
rs323868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323873	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	1.00[ASN][1000 genomes]
rs323885	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323886	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323887	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323890	0.90[AMR][1000 genomes]
rs323892	1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes]
rs323893	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323895	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323897	1.00[MEX][hapmap];0.81[MKK][hapmap]
rs323898	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs379462	1.00[MEX][hapmap];0.83[YRI][hapmap]
rs403620	0.90[AMR][1000 genomes]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56715917	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs7432986	1.00[MEX][hapmap]
rs7614743	0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51987600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:51977200-51989200	Weak transcription	Ovary	ovary
3	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
4	chr3:51977400-51986200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:51977400-51987200	Weak transcription	Fetal Lung	lung
6	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
7	chr3:51977600-51986000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:51977600-51987200	Weak transcription	HSMMtube	muscle
9	chr3:51977600-51987600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:51977600-51987600	Weak transcription	HSMM	muscle
11	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
13	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
14	chr3:51977800-51985600	Weak transcription	Stomach Mucosa	stomach
15	chr3:51977800-51986000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:51977800-51987200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:51977800-51987800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:51978800-51985200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:51978800-51987000	Weak transcription	Hela-S3	cervix
21	chr3:51979000-51987200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:51979200-51986000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:51979800-51987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:51980400-51989400	Weak transcription	Right Ventricle	heart
25	chr3:51980600-51989200	Weak transcription	Gastric	stomach
26	chr3:51980800-51987200	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:51980800-51988000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:51982400-51987400	Weak transcription	Fetal Intestine Small	intestine
29	chr3:51982400-51987800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:51982600-51986200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:51982600-51986600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:51983000-51987200	Weak transcription	Osteobl	bone
33	chr3:51983400-51987000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:51983400-51988400	Weak transcription	Colonic Mucosa	Colon
35	chr3:51983400-51989000	Weak transcription	Brain Anterior Caudate	brain
36	chr3:51983400-51989000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:51983400-51989000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:51983400-51989400	Weak transcription	Lung	lung
39	chr3:51983600-51986000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:51983600-51986600	Weak transcription	Fetal Stomach	stomach
41	chr3:51983600-51987200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:51983600-51987200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:51983600-51987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:51983600-51987800	Weak transcription	NHLF	lung
45	chr3:51983600-51989000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:51983600-51989200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:51983600-51989200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:51983600-51989200	Weak transcription	Spleen	Spleen
49	chr3:51983800-51987200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:51983800-51987200	Weak transcription	Brain Angular Gyrus	brain

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