Variant report

Variant	rs6691539
Chromosome Location	chr1:247372672-247372673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:247372485-247373262	GM12878	blood:	n/a	n/a
2	MXI1	chr1:247372272-247375223	SK-N-SH	brain:	n/a	n/a
3	BRCA1	chr1:247372559-247372685	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:247372362-247372950	GM12878	blood:	n/a	n/a
5	MAX	chr1:247372660-247372990	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247366973..247371599-chr1:247371697..247375755,6	MCF-7	breast:
2	chr1:247338400..247340247-chr1:247370932..247373277,2	K562	blood:
3	chr1:247371399..247373319-chr1:247494315..247496686,3	K562	blood:
4	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
5	chr1:247361273..247363730-chr1:247370221..247373518,3	K562	blood:
6	chr1:247274493..247276812-chr1:247371838..247375899,3	K562	blood:
7	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
8	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP82	TF binding region
ENSG00000162714	Chromatin interaction
ENSG00000252516	Chromatin interaction
ENSG00000224014	Chromatin interaction
ENSG00000221953	Chromatin interaction
ENSG00000227671	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10754539	1.00[ASW][hapmap]
rs11811599	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1343544	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2793289	0.82[ASW][hapmap]
rs4314914	0.89[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55768801	0.96[EUR][1000 genomes]
rs56338561	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57861883	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60050650	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61636449	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6680707	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6693807	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6699577	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704060	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
10	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6691539	MIR3916	cis	Whole Blood	GTEx
rs6691539	LOC729806	Cis_1M	lymphoblastoid	RTeQTL
rs6691539	RP11-488L18.10	cis	Esophagus Mucosa	GTEx
rs6691539	RP11-488L18.10	cis	lung	GTEx
rs6691539	ZNF496	cis	cerebellum	SCAN
rs6691539	RP11-488L18.10	cis	Artery Tibial	GTEx
rs6691539	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247362400-247373400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:247362600-247372800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:247363600-247372800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:247365600-247372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:247369000-247372800	ZNF genes & repeats	A549	lung
6	chr1:247370800-247372800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:247371000-247372800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr1:247371000-247372800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:247371200-247372800	Enhancers	HepG2	liver
10	chr1:247371200-247373000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:247371400-247372800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:247371600-247372800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:247371800-247373200	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:247372000-247372800	Enhancers	Primary B cells from cord blood	blood
15	chr1:247372000-247373000	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:247372000-247373000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:247372000-247373600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr1:247372200-247373000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:247372200-247373000	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr1:247372200-247373200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:247372200-247373200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:247372200-247373400	Enhancers	Stomach Mucosa	stomach
23	chr1:247372200-247373600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr1:247372200-247373600	Flanking Active TSS	Hela-S3	cervix
25	chr1:247372400-247372800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:247372400-247372800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr1:247372400-247372800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:247372400-247372800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr1:247372400-247372800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:247372400-247372800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:247372400-247372800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:247372400-247372800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:247372400-247372800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:247372400-247372800	Enhancers	Brain Anterior Caudate	brain
35	chr1:247372400-247372800	Genic enhancers	Lung	lung
36	chr1:247372400-247372800	Enhancers	Pancreas	Pancrea
37	chr1:247372400-247372800	Enhancers	Psoas Muscle	Psoas
38	chr1:247372400-247372800	Enhancers	Right Ventricle	heart
39	chr1:247372400-247372800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr1:247372400-247372800	Flanking Active TSS	HSMM	muscle
41	chr1:247372400-247372800	Active TSS	HSMMtube	muscle
42	chr1:247372400-247373000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr1:247372400-247373000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:247372400-247373000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:247372400-247373000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:247372400-247373000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
47	chr1:247372400-247373000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
48	chr1:247372400-247373000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:247372400-247373000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:247372400-247373000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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