Variant report

Variant	rs11943130
Chromosome Location	chr4:78123574-78123575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78116886..78120148-chr4:78122009..78124874,3	K562	blood:
2	chr4:78122483..78124874-chr4:78125132..78127042,2	MCF-7	breast:
3	chr4:78077855..78079830-chr4:78121652..78124230,4	MCF-7	breast:
4	chr4:77995909..77997574-chr4:78122547..78125037,2	MCF-7	breast:
5	chr4:77993291..77996240-chr4:78123279..78125310,2	K562	blood:
6	chr4:78119460..78121220-chr4:78122778..78124442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138764	Chromatin interaction
ENSG00000118816	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10006360	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10010725	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10014391	0.93[ASN][1000 genomes]
rs10017796	0.95[ASN][1000 genomes]
rs10017878	0.93[ASN][1000 genomes]
rs10022252	0.95[ASN][1000 genomes]
rs10027894	0.95[ASN][1000 genomes]
rs10028268	0.91[GIH][hapmap]
rs1006041	0.97[ASN][1000 genomes]
rs10518167	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[ASN][1000 genomes]
rs17002416	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17002418	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17002420	1.00[CEU][hapmap]
rs17393572	1.00[JPT][hapmap]
rs28367533	0.95[ASN][1000 genomes]
rs28373623	0.95[ASN][1000 genomes]
rs28416544	0.95[ASN][1000 genomes]
rs28470363	0.95[ASN][1000 genomes]
rs28526402	0.95[ASN][1000 genomes]
rs28693444	0.95[ASN][1000 genomes]
rs28697073	0.95[ASN][1000 genomes]
rs28718050	0.95[ASN][1000 genomes]
rs4150060	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4150063	1.00[CEU][hapmap]
rs4150092	0.85[ASN][1000 genomes]
rs4150099	0.85[ASN][1000 genomes]
rs4150103	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4293811	1.00[JPT][hapmap]
rs58288213	0.95[ASN][1000 genomes]
rs58507229	0.86[ASN][1000 genomes]
rs59124751	1.00[ASN][1000 genomes]
rs59757896	0.93[ASN][1000 genomes]
rs6822800	1.00[JPT][hapmap]
rs6823048	0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6848898	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs6851055	0.95[ASN][1000 genomes]
rs6852578	0.95[ASN][1000 genomes]
rs72861687	0.95[ASN][1000 genomes]
rs72861692	1.00[ASN][1000 genomes]
rs72861694	1.00[ASN][1000 genomes]
rs72863250	1.00[ASN][1000 genomes]
rs72863264	0.97[ASN][1000 genomes]
rs72863265	0.97[ASN][1000 genomes]
rs72863270	0.97[ASN][1000 genomes]
rs9307246	0.95[ASN][1000 genomes]
rs9654188	0.95[ASN][1000 genomes]
rs9654189	0.95[ASN][1000 genomes]
rs9654190	0.95[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	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1011551	chr4:78120872-78204224	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1012298	chr4:78120872-78255427	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11943130	PAQR3	cis	cerebellum	SCAN
rs11943130	PRKCZ	trans	lymphoblastoid	seeQTL
rs11943130	PF4V1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78116400-78124600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:78118800-78124600	Weak transcription	Fetal Thymus	thymus
3	chr4:78119200-78124400	Weak transcription	Primary B cells from cord blood	blood
4	chr4:78119200-78124600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:78120400-78124800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:78120600-78125200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:78121000-78123600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:78121200-78123800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:78121600-78123600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:78121600-78124600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:78122400-78125000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:78122600-78124800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:78122600-78125200	Enhancers	Stomach Mucosa	stomach
14	chr4:78122800-78124000	Flanking Active TSS	NHEK	skin
15	chr4:78122800-78124800	Enhancers	Fetal Intestine Large	intestine
16	chr4:78122800-78125400	Enhancers	HSMM	muscle
17	chr4:78123000-78123600	Flanking Active TSS	HMEC	breast
18	chr4:78123000-78123800	Enhancers	Hela-S3	cervix
19	chr4:78123000-78124800	Enhancers	Fetal Intestine Small	intestine
20	chr4:78123200-78124600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:78123200-78124600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:78123400-78124600	Weak transcription	Primary T cells from cord blood	blood
23	chr4:78123400-78124800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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