Variant report

Variant	rs4518274
Chromosome Location	chr4:78069066-78069067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77996103..77998290-chr4:78066970..78070859,4	MCF-7	breast:
2	chr4:77994701..77998612-chr4:78066098..78069979,6	MCF-7	breast:
3	chr4:78067084..78069572-chr4:78071831..78074311,3	MCF-7	breast:
4	chr4:77995679..77998060-chr4:78068555..78071849,3	K562	blood:
5	chr4:78066677..78070110-chr4:78071509..78075152,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201641	Chromatin interaction
ENSG00000118816	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10025838	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1006042	0.84[GIH][hapmap]
rs11097704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724432	0.86[JPT][hapmap]
rs11731592	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12504752	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12509168	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12640093	0.96[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs28464714	0.89[ASN][1000 genomes]
rs28503908	0.86[JPT][hapmap]
rs4241604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4280759	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4302483	0.86[JPT][hapmap]
rs4365751	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4382065	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4544732	0.86[JPT][hapmap]
rs4547817	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4558892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4563522	0.90[EUR][1000 genomes]
rs4859473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859751	0.86[JPT][hapmap]
rs4859756	0.92[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6532867	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532868	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532870	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6532871	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6846698	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6849124	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6849534	0.84[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7654920	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4518274	CCNG2	cis	cerebellum	SCAN
rs4518274	BMP3	cis	parietal	SCAN
rs4518274	TMPRSS2	trans	cerebellum	SCAN
rs4518274	PAQR3	cis	cerebellum	SCAN
rs4518274	PF4V1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78065600-78069200	Enhancers	Fetal Intestine Large	intestine
2	chr4:78065800-78069400	Enhancers	Fetal Intestine Small	intestine
3	chr4:78066400-78069400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:78066400-78069800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr4:78067000-78069200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr4:78067400-78073400	Weak transcription	GM12878-XiMat	blood
7	chr4:78067600-78069200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:78067600-78069200	Enhancers	HSMMtube	muscle
9	chr4:78067600-78069400	Enhancers	Hela-S3	cervix
10	chr4:78067600-78070000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr4:78067600-78073600	Weak transcription	Placenta	Placenta
12	chr4:78067800-78069200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:78067800-78073200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:78067800-78073400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:78067800-78077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:78068000-78070400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr4:78068000-78076000	Weak transcription	HMEC	breast
18	chr4:78068200-78070800	Weak transcription	Small Intestine	intestine
19	chr4:78068200-78073400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:78068200-78073400	Weak transcription	Thymus	Thymus
21	chr4:78068200-78073600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:78068200-78073600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:78068200-78073600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:78068200-78073600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:78068200-78073600	Weak transcription	Stomach Mucosa	stomach
26	chr4:78068200-78073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:78068200-78075200	Weak transcription	NHEK	skin
28	chr4:78068400-78072000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:78068600-78072400	Weak transcription	Primary B cells from cord blood	blood
30	chr4:78068600-78073200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:78068600-78073200	Weak transcription	Fetal Lung	lung
32	chr4:78068600-78073400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:78068600-78075800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:78068600-78076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:78068800-78073200	Weak transcription	Primary T cells from cord blood	blood
36	chr4:78068800-78073400	Weak transcription	Fetal Kidney	kidney
37	chr4:78068800-78074000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:78068800-78074600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:78069000-78069200	Enhancers	Fetal Thymus	thymus
40	chr4:78069000-78069400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:78069000-78069400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:78069000-78069400	Enhancers	Duodenum Mucosa	Duodenum
43	chr4:78069000-78069400	Enhancers	Psoas Muscle	Psoas
44	chr4:78069000-78073400	Weak transcription	Primary hematopoietic stem cells	blood

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