Variant report

Variant	rs7645622
Chromosome Location	chr3:145887759-145887760
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145881041..145885690-chr3:145886054..145890900,6	MCF-7	breast:
2	chr3:145876765..145880789-chr3:145885972..145889074,4	MCF-7	breast:
3	chr3:145886536..145888429-chr3:145902390..145904087,2	MCF-7	breast:
4	chr3:145885862..145887990-chr3:145898381..145900841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11923433	0.82[CEU][hapmap];0.82[CHD][hapmap]
rs12496198	0.91[CHB][hapmap]
rs12496358	0.91[CHB][hapmap]
rs1355685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449440	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs1449444	0.91[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap]
rs1449445	0.91[CHB][hapmap]
rs1449450	0.91[CHB][hapmap]
rs1512900	0.91[CHB][hapmap]
rs1613698	0.90[CHB][hapmap];0.82[GIH][hapmap]
rs1707465	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs1900926	0.91[CHB][hapmap]
rs2029137	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs2864793	0.91[CHB][hapmap]
rs35399421	0.83[ASN][1000 genomes]
rs3792339	0.91[CHB][hapmap]
rs3792341	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs3804660	0.90[CHB][hapmap]
rs3804661	0.91[CHB][hapmap]
rs3804664	0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs3804665	0.90[CHB][hapmap];0.83[GIH][hapmap]
rs3804666	0.91[CHB][hapmap]
rs3804669	0.91[CHB][hapmap]
rs3816399	0.91[CHB][hapmap]
rs4681294	0.91[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap]
rs4681299	0.91[CHB][hapmap]
rs6710	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs6783601	0.91[CHB][hapmap]
rs6793380	0.85[ASN][1000 genomes]
rs6799720	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs6800434	0.90[CHB][hapmap]
rs6801418	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs6802384	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs7431590	0.91[CHB][hapmap]
rs7614409	0.91[CHB][hapmap];0.83[GIH][hapmap]
rs7641322	0.83[ASN][1000 genomes]
rs764755	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs895929	0.91[CHB][hapmap]
rs895930	0.91[CHB][hapmap]
rs9289713	0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap]
rs9289714	0.91[CHB][hapmap]
rs9289716	0.91[CHB][hapmap];0.92[GIH][hapmap]
rs9289718	0.91[CHB][hapmap]
rs959329	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs9809099	0.91[CHB][hapmap]
rs9813047	0.90[CHB][hapmap]
rs9828112	0.90[CHB][hapmap]
rs9842036	0.91[CHB][hapmap]
rs9852153	0.90[CHB][hapmap]
rs9862237	0.91[CHB][hapmap]
rs9865802	0.91[CHB][hapmap]
rs9874388	0.86[CHB][hapmap];0.81[GIH][hapmap]
rs9877411	0.90[CHB][hapmap]
rs9878166	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7645622	HLTF	cis	parietal	SCAN
rs7645622	MAP3K5	trans	cerebellum	SCAN
rs7645622	PLOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145880800-145914400	Weak transcription	Left Ventricle	heart
2	chr3:145883000-145913000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:145883800-145890000	Weak transcription	Fetal Heart	heart
4	chr3:145884000-145903400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:145884800-145910800	Weak transcription	Liver	Liver
6	chr3:145885000-145887800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:145885000-145908000	Weak transcription	Aorta	Aorta
8	chr3:145885400-145895400	Weak transcription	HSMM	muscle
9	chr3:145885600-145907800	Weak transcription	Ovary	ovary
10	chr3:145886200-145890200	Weak transcription	Osteobl	bone

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