Variant report

Variant	rs4946724
Chromosome Location	chr6:106538695-106538696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:106538067..106540230-chr6:106542190..106543690,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1010273	0.91[AMR][1000 genomes]
rs12175062	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]
rs1340064	0.81[JPT][hapmap]
rs1934593	0.90[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	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946722	0.81[CEU][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946725	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs535780	0.81[JPT][hapmap]
rs547057	0.86[JPT][hapmap]
rs6910095	1.00[ASW][hapmap]
rs6924535	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9373832	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946724	PRDM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106533600-106539400	Active TSS	Duodenum Mucosa	Duodenum
2	chr6:106533600-106541200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr6:106534200-106539200	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr6:106535600-106539200	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:106536000-106539200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:106536200-106545800	Weak transcription	Spleen	Spleen
7	chr6:106536400-106539200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:106536400-106545200	Weak transcription	HSMMtube	muscle
9	chr6:106536400-106545600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:106536600-106539000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:106537000-106538800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:106537000-106540000	Weak transcription	Small Intestine	intestine
13	chr6:106537000-106543400	Weak transcription	NHEK	skin
14	chr6:106537000-106545000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:106537200-106539400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr6:106537200-106545200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:106537400-106539200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:106537400-106544200	Weak transcription	Dnd41	blood
19	chr6:106537400-106544400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:106537400-106545000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:106537400-106545200	Weak transcription	Psoas Muscle	Psoas
22	chr6:106537400-106545200	Weak transcription	HSMM	muscle
23	chr6:106537600-106539200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:106537800-106539000	Weak transcription	Esophagus	oesophagus
25	chr6:106537800-106539200	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:106537800-106539200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:106537800-106545600	Weak transcription	Lung	lung
28	chr6:106538000-106538800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr6:106538000-106538800	Active TSS	A549	lung
30	chr6:106538000-106539000	Active TSS	Primary T cells fromperipheralblood	blood
31	chr6:106538000-106539400	Flanking Active TSS	GM12878-XiMat	blood
32	chr6:106538000-106539800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:106538000-106545200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:106538200-106539000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:106538200-106539200	Genic enhancers	HMEC	breast
36	chr6:106538200-106545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:106538400-106538800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:106538400-106538800	Enhancers	Osteobl	bone
39	chr6:106538400-106539000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:106538400-106539000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:106538400-106539000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:106538400-106539000	Weak transcription	Fetal Intestine Small	intestine
43	chr6:106538400-106542000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:106538400-106543200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:106538600-106539000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:106538600-106539000	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:106538600-106539200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr6:106538600-106539200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr6:106538600-106539200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:106538600-106539200	Enhancers	NHDF-Ad	bronchial

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