Variant report

Variant	rs1670545
Chromosome Location	chr11:73586112-73586113
allele	C/G
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	chr11:73585876-73588793	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr11:73585989-73587043	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:73586074-73586974	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:73586022-73587172	GM12891	blood:	n/a	n/a
5	POLR2A	chr11:73585952-73586718	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:73585707-73586807	K562	blood:	n/a	n/a
7	POLR2A	chr11:73585758-73588498	GM12892	blood:	n/a	n/a
8	SRF	chr11:73585976-73586157	HepG2	liver:	n/a	chr11:73586065-73586076 chr11:73586063-73586076 chr11:73586058-73586075 chr11:73586062-73586077 chr11:73586065-73586074 chr11:73586063-73586074 chr11:73586061-73586079 chr11:73586064-73586081 chr11:73586059-73586077 chr11:73586064-73586075 chr11:73586065-73586079 chr11:73586061-73586078
9	POLR2A	chr11:73585961-73586670	GM12891	blood:	n/a	n/a
10	POLR2A	chr11:73585925-73586672	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr11:73586039-73588558	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:73585923-73588429	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:73585928-73588368	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:73585925-73586670	GM12892	blood:	n/a	n/a
15	POLR2A	chr11:73585872-73586699	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr11:73584983-73586623	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73584965..73587189-chr11:73691735..73694698,2	K562	blood:
2	chr11:73497415..73503223-chr11:73585602..73589591,8	K562	blood:
3	chr11:73585766..73589510-chr11:73599101..73602813,5	MCF-7	breast:

Variant related genes	Relation type
PAAF1	TF binding region
COA4	TF binding region
ENSG00000175567	Chromatin interaction
ENSG00000175581	Chromatin interaction
ENSG00000175575	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10898948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10898950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11235932	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs1670546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1670558	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3018335	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4362170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7105293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1670545	WDR71	cis	multi-tissue	Pritchard
rs1670545	FLJ11848	cis	multi-tissue	Pritchard
rs1670545	PAAF1	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73571600-73586200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:73573000-73586200	Weak transcription	Fetal Brain Male	brain
3	chr11:73578000-73586400	Weak transcription	Fetal Heart	heart
4	chr11:73578800-73586200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:73579200-73586400	Weak transcription	Small Intestine	intestine
6	chr11:73579400-73586200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:73579600-73586200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:73579600-73586200	Strong transcription	Fetal Stomach	stomach
9	chr11:73579600-73586200	Strong transcription	Thymus	Thymus
10	chr11:73579800-73586200	Strong transcription	Primary hematopoietic stem cells	blood
11	chr11:73579800-73586200	Strong transcription	Fetal Lung	lung
12	chr11:73580200-73586200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:73580200-73586200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:73580200-73586600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:73580400-73586200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:73580400-73586200	Strong transcription	Primary T cells from cord blood	blood
17	chr11:73580400-73586200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:73580400-73586200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:73580800-73586200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr11:73580800-73586600	Weak transcription	Stomach Mucosa	stomach
21	chr11:73581400-73586400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:73581600-73586200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:73581600-73586200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr11:73581800-73586200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:73582200-73586200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr11:73582200-73586200	Strong transcription	Osteobl	bone
27	chr11:73582400-73586200	Strong transcription	Brain Germinal Matrix	brain
28	chr11:73582400-73586400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:73582600-73586200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:73582600-73586200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:73583200-73586200	Strong transcription	Rectal Smooth Muscle	rectum
32	chr11:73584000-73586400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:73584400-73586200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:73584400-73586400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:73584400-73586800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:73584400-73586800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:73584400-73587200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr11:73584400-73587200	Weak transcription	Aorta	Aorta
39	chr11:73584800-73586200	Enhancers	HSMMtube	muscle
40	chr11:73584800-73586200	Weak transcription	NH-A	brain
41	chr11:73584800-73586400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:73584800-73586400	Weak transcription	Psoas Muscle	Psoas
43	chr11:73585000-73586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:73585000-73586200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr11:73585000-73586200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:73585000-73586200	Weak transcription	Brain Anterior Caudate	brain
47	chr11:73585000-73586200	Genic enhancers	HepG2	liver
48	chr11:73585000-73586200	Genic enhancers	HSMM	muscle
49	chr11:73585000-73586200	Weak transcription	NHDF-Ad	bronchial
50	chr11:73585000-73586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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