Variant report

Variant	rs4859756
Chromosome Location	chr4:78124348-78124349
allele	G/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	chr4:77997759..78000070-chr4:78123881..78125820,2	MCF-7	breast:
3	chr4:78122483..78124874-chr4:78125132..78127042,2	MCF-7	breast:
4	chr4:77968037..77968611-chr4:78124042..78125032,2	MCF-7	breast:
5	chr4:77995909..77997574-chr4:78122547..78125037,2	MCF-7	breast:
6	chr4:77993291..77996240-chr4:78123279..78125310,2	K562	blood:
7	chr4:78119460..78121220-chr4:78122778..78124442,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118816	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10009384	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10010290	0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10018359	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10025838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026129	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10030727	0.96[ASN][1000 genomes]
rs10030735	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10030867	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10030957	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1006042	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10856957	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11097704	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11097730	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11731592	0.87[EUR][1000 genomes]
rs12504752	0.81[EUR][1000 genomes]
rs12508219	0.81[JPT][hapmap]
rs12509168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640093	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1477314	0.91[JPT][hapmap]
rs1559119	0.91[JPT][hapmap]
rs1559122	0.89[JPT][hapmap]
rs2042228	0.91[JPT][hapmap]
rs4241604	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4280759	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4365751	0.84[EUR][1000 genomes]
rs4518274	0.92[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4547817	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4558892	0.83[EUR][1000 genomes]
rs4563522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4576030	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4582179	0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4582180	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4859473	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs4859475	0.85[JPT][hapmap]
rs4859477	0.90[JPT][hapmap]
rs4859753	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859754	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4859755	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs6532867	0.87[EUR][1000 genomes]
rs6532868	0.87[EUR][1000 genomes]
rs6532870	0.88[EUR][1000 genomes]
rs6532871	0.88[EUR][1000 genomes]
rs6822794	0.91[JPT][hapmap]
rs6840915	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6845599	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6845942	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6846698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6849124	0.84[CEU][hapmap]
rs6849534	0.84[CEU][hapmap]
rs6857792	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7690427	0.86[JPT][hapmap]

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
rs4859756	PF4V1	cis	cerebellum	SCAN
rs4859756	BMP3	cis	parietal	SCAN
rs4859756	CCNG2	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr4:78121600-78124600	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:78122400-78125000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:78122600-78124800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr4:78122600-78125200	Enhancers	Stomach Mucosa	stomach
11	chr4:78122800-78124800	Enhancers	Fetal Intestine Large	intestine
12	chr4:78122800-78125400	Enhancers	HSMM	muscle
13	chr4:78123000-78124800	Enhancers	Fetal Intestine Small	intestine
14	chr4:78123200-78124600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:78123200-78124600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:78123400-78124600	Weak transcription	Primary T cells from cord blood	blood
17	chr4:78123400-78124800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:78123600-78124800	Enhancers	Duodenum Mucosa	Duodenum
19	chr4:78123600-78124800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr4:78123600-78125200	Enhancers	HMEC	breast
21	chr4:78124000-78124400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:78124000-78124800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr4:78124000-78125200	Enhancers	NHEK	skin
24	chr4:78124200-78125200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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