Variant report

Variant	rs6875595
Chromosome Location	chr5:118748742-118748743
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118322603..118326136-chr5:118745091..118748767,5	MCF-7	breast:
2	chr5:118323143..118324569-chr5:118747458..118748790,7	MCF-7	breast:
3	chr5:118747162..118749496-chr5:118752473..118755239,2	K562	blood:
4	chr5:118602609..118607395-chr5:118746240..118749056,4	MCF-7	breast:
5	chr5:118746206..118749496-chr5:118750368..118755239,5	K562	blood:

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1112247	0.80[GIH][hapmap]
rs2259347	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2451804	0.85[EUR][1000 genomes]
rs2451816	0.86[CHB][hapmap]
rs2451818	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2457221	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2546210	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs25640	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs257970	0.86[CHB][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs257972	0.90[CHB][hapmap]
rs257973	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap]
rs257974	0.86[CHB][hapmap]
rs257981	0.85[EUR][1000 genomes]
rs258049	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs258052	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs26180	0.91[CHB][hapmap]
rs26181	0.91[MEX][hapmap]
rs26184	0.91[MEX][hapmap]
rs2636968	0.91[MEX][hapmap]
rs2945327	0.82[CHB][hapmap]
rs32658	0.82[GIH][hapmap]
rs32659	0.86[CHB][hapmap]
rs32662	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs32665	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs408095	0.82[GIH][hapmap]
rs426899	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs455318	0.92[EUR][1000 genomes]
rs455949	0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs457106	0.81[GIH][hapmap]
rs461108	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs462756	0.92[EUR][1000 genomes]
rs463098	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap]
rs465091	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4895191	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895371	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4895372	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7720373	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7720678	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7721602	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv965533	chr5:118738884-118762384	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6875595	PRR16	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118707600-118754600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:118747800-118753400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:118748000-118748800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:118748000-118748800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr5:118748000-118748800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:118748000-118748800	Enhancers	Brain Germinal Matrix	brain
7	chr5:118748000-118748800	Enhancers	Hela-S3	cervix
8	chr5:118748000-118749200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr5:118748000-118749200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:118748000-118749400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:118748000-118749800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:118748000-118749800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr5:118748000-118750400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:118748000-118750800	Enhancers	Primary B cells from cord blood	blood
15	chr5:118748000-118752200	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:118748000-118752600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:118748000-118753600	Weak transcription	HMEC	breast
18	chr5:118748000-118753600	Weak transcription	NH-A	brain
19	chr5:118748000-118753800	Weak transcription	NHEK	skin
20	chr5:118748000-118754000	Weak transcription	Esophagus	oesophagus
21	chr5:118748000-118754400	Weak transcription	Placenta	Placenta
22	chr5:118748000-118755400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:118748200-118748800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:118748200-118748800	Enhancers	Brain Angular Gyrus	brain
25	chr5:118748200-118748800	Enhancers	A549	lung
26	chr5:118748200-118749200	Enhancers	HepG2	liver
27	chr5:118748200-118749800	Weak transcription	GM12878-XiMat	blood
28	chr5:118748200-118750400	Enhancers	Stomach Mucosa	stomach
29	chr5:118748200-118752600	Weak transcription	K562	blood
30	chr5:118748200-118753200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:118748200-118753200	Weak transcription	Dnd41	blood
32	chr5:118748200-118753400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:118748200-118753400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:118748200-118753600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:118748200-118753600	Weak transcription	Primary T cells from cord blood	blood
36	chr5:118748200-118753600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:118748200-118753600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:118748200-118753600	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:118748200-118755000	Weak transcription	Liver	Liver
40	chr5:118748600-118748800	Enhancers	Colonic Mucosa	Colon
41	chr5:118748600-118748800	Enhancers	Duodenum Mucosa	Duodenum
42	chr5:118748600-118748800	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr5:118748600-118753400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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