Variant report

Variant	rs6784998
Chromosome Location	chr3:142454414-142454415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142446381..142451042-chr3:142452461..142456745,6	MCF-7	breast:
2	chr3:142295544..142297726-chr3:142454220..142455765,2	K562	blood:
3	chr3:142449190..142450946-chr3:142453466..142455123,2	K562	blood:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11715459	0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11915805	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1382688	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs1604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1871349	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2033912	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2177398	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs28571594	0.89[AMR][1000 genomes]
rs28689551	0.91[ASN][1000 genomes]
rs35467195	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35862982	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3844273	0.90[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs4539980	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4643748	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs55722917	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56775607	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59108985	0.91[ASN][1000 genomes]
rs6440104	0.81[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs6440106	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440107	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440108	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs6440110	0.88[ASN][1000 genomes]
rs6772222	0.91[ASN][1000 genomes]
rs6790959	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6803681	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7621642	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.91[ASN][1000 genomes]
rs7623762	0.94[ASW][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs7626908	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628728	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7629129	0.85[AMR][1000 genomes]
rs7638459	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs7639403	0.89[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.91[ASN][1000 genomes]
rs7644704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7647291	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653309	0.91[ASN][1000 genomes]
rs953239	0.96[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9820721	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823836	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824476	0.91[ASN][1000 genomes]
rs9835135	0.90[ASN][1000 genomes]
rs9836269	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9849461	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs9851381	0.90[CHB][hapmap]
rs9861598	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864230	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9865053	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6784998	PLS1	cis	cerebellum	SCAN
rs6784998	ZIC1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142444200-142467400	Weak transcription	HSMM	muscle
2	chr3:142444400-142467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:142444400-142469600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:142444600-142467200	Weak transcription	NH-A	brain
5	chr3:142445000-142467400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:142445000-142467800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:142445000-142479000	Weak transcription	Fetal Brain Female	brain
8	chr3:142445200-142467000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:142445200-142467000	Weak transcription	NHDF-Ad	bronchial
10	chr3:142445200-142467000	Weak transcription	Osteobl	bone
11	chr3:142445200-142467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:142445200-142467400	Weak transcription	HMEC	breast
13	chr3:142445400-142467200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:142445800-142467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:142446000-142467000	Weak transcription	A549	lung
16	chr3:142446400-142467200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:142448400-142455200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:142450200-142467000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:142451400-142467200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:142451600-142467000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:142451800-142467600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:142452000-142467200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:142452800-142489000	Weak transcription	Aorta	Aorta
24	chr3:142453600-142467200	Weak transcription	Left Ventricle	heart
25	chr3:142453800-142454600	Enhancers	Fetal Heart	heart
26	chr3:142454000-142454600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:142454400-142454600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:142454400-142454600	Enhancers	Ovary	ovary
29	chr3:142454400-142454600	Enhancers	Right Ventricle	heart
30	chr3:142454400-142454800	Enhancers	Fetal Brain Male	brain

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