Variant report

Variant	rs12175062
Chromosome Location	chr6:106544560-106544561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:106544453-106547850	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106543067..106545717-chr6:106603091..106604835,2	K562	blood:

Variant related genes	Relation type
PRDM1	TF binding region
ENSG00000269919	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1010273	0.97[AMR][1000 genomes]
rs1340064	0.81[JPT][hapmap]
rs1934593	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1984224	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1985899	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946722	0.91[CEU][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946724	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946725	0.90[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs535780	0.81[JPT][hapmap]
rs547057	0.86[JPT][hapmap]
rs6924535	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9373832	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12175062	PRDM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106536200-106545800	Weak transcription	Spleen	Spleen
2	chr6:106536400-106545200	Weak transcription	HSMMtube	muscle
3	chr6:106536400-106545600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:106537000-106545000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:106537200-106545200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:106537400-106545000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:106537400-106545200	Weak transcription	Psoas Muscle	Psoas
8	chr6:106537400-106545200	Weak transcription	HSMM	muscle
9	chr6:106537800-106545600	Weak transcription	Lung	lung
10	chr6:106538000-106545200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:106538200-106545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:106538600-106544800	Weak transcription	NHLF	lung
13	chr6:106538600-106545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:106538600-106545000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:106539200-106545000	Weak transcription	HMEC	breast
16	chr6:106539200-106545200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:106539200-106545400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:106539200-106545400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:106540400-106545400	Weak transcription	Esophagus	oesophagus
20	chr6:106540600-106544800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:106540600-106545000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr6:106540800-106544600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:106541000-106544800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:106541200-106544600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:106541200-106545000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:106541400-106545000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr6:106541800-106544600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:106541800-106545600	Weak transcription	Small Intestine	intestine
29	chr6:106542400-106544800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:106542600-106544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:106542600-106545000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:106542800-106545000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr6:106542800-106545200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:106542800-106545200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:106542800-106548600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:106543000-106544600	Weak transcription	Primary B cells from cord blood	blood
37	chr6:106543000-106544600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:106543000-106545000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:106543600-106544600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:106543600-106545600	Genic enhancers	Fetal Intestine Large	intestine
41	chr6:106543600-106549600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:106543800-106544600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:106543800-106544600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:106543800-106545000	Weak transcription	NHEK	skin
45	chr6:106544000-106544600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:106544000-106545000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:106544000-106545000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr6:106544000-106545000	Weak transcription	Osteobl	bone
49	chr6:106544000-106545200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:106544000-106545200	Weak transcription	NH-A	brain

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