Variant report

Variant	rs13242458
Chromosome Location	chr7:99695131-99695132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99694688-99696323	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:99694831-99695224	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr7:99694796-99695262	GM12878	blood:	n/a	n/a
4	POLR2A	chr7:99694417-99699772	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr7:99694796-99696431	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:99694735-99695619	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:99694779-99695459	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr7:99694703-99697612	GM12892	blood:	n/a	n/a
9	ATF2	chr7:99694750-99695379	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF2	chr7:99694799-99695916	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr7:99694731-99695187	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:99694640-99696904	K562	blood:	n/a	n/a
13	POLR2A	chr7:99694653-99697678	H1-hESC	embryonic stem cell:	n/a	n/a
14	HEY1	chr7:99694628-99697652	K562	blood:	n/a	chr7:99695196-99695205
15	POLR2A	chr7:99687998-99697728	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr7:99694777-99696253	A549	lung:	n/a	n/a
17	POLR2A	chr7:99694703-99695446	HL-60	blood:	n/a	n/a
18	POLR2A	chr7:99694897-99695166	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:99694639-99695381	K562	blood:	n/a	n/a
20	POLR2A	chr7:99694633-99695460	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr7:99694683-99696815	K562	blood:	n/a	n/a
22	POLR2A	chr7:99687562-99696983	HepG2	liver:	n/a	n/a
23	POLR2A	chr7:99694865-99695460	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:99694702-99697727	K562	blood:	n/a	n/a
25	POLR2A	chr7:99694608-99696959	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr7:99694646-99700079	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr7:99694505-99700789	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr7:99695090-99695184	MCF-7	breast:	n/a	n/a
29	HEY1	chr7:99694832-99695262	K562	blood:	n/a	chr7:99695196-99695205
30	POLR2A	chr7:99694841-99695836	Hela-S3	cervix:	n/a	n/a
31	TEAD4	chr7:99694944-99695528	K562	blood:	n/a	n/a
32	POLR2A	chr7:99694762-99695338	K562	blood:	n/a	n/a
33	POLR2A	chr7:99694805-99695253	GM12891	blood:	n/a	n/a
34	POLR2A	chr7:99694559-99697007	GM12892	blood:	n/a	n/a
35	POLR2A	chr7:99694630-99695581	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr7:99694635-99697617	K562	blood:	n/a	n/a
37	POLR2A	chr7:99694990-99696427	HL-60	blood:	n/a	n/a
38	POLR2A	chr7:99694572-99696494	K562	blood:	n/a	n/a
39	POLR2A	chr7:99694689-99697009	GM12892	blood:	n/a	n/a
40	POLR2A	chr7:99694773-99695425	GM12891	blood:	n/a	n/a
41	POLR2A	chr7:99694897-99695293	GM12892	blood:	n/a	n/a
42	POLR2A	chr7:99694793-99696820	K562	blood:	n/a	n/a
43	POLR2A	chr7:99694594-99699682	GM12878	blood:	n/a	n/a
44	POLR2A	chr7:99694627-99695161	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr7:99694577-99700301	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr7:99694759-99695334	GM12891	blood:	n/a	n/a
47	ATF2	chr7:99694683-99695150	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
MCM7	TF binding region
MIR25	TF binding region
MIR93	TF binding region
MIR106B	TF binding region
AP4M1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12705069	0.85[EUR][1000 genomes]
rs12705074	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes]
rs34065606	0.88[AMR][1000 genomes]
rs34312198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34766893	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6955348	1.00[ASW][hapmap];0.92[GIH][hapmap];0.82[AMR][1000 genomes]
rs73156680	1.00[AFR][1000 genomes]
rs73156683	1.00[AFR][1000 genomes]
rs73158413	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13242458	PMPCB	cis	parietal	SCAN
rs13242458	ZSCAN21	cis	parietal	SCAN
rs13242458	ACTL6B	cis	parietal	SCAN
rs13242458	AP4M1	cis	multi-tissue	Pritchard
rs13242458	PILRB	cis	cerebellum	SCAN
rs13242458	AP4M1	cis	cerebellum	SCAN
rs13242458	TIMP1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99687400-99697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99687600-99696000	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr7:99687600-99696600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:99687600-99696800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:99687800-99696000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:99687800-99696600	Strong transcription	Fetal Intestine Small	intestine
7	chr7:99688000-99695400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:99688000-99695600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:99688000-99695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:99688000-99696000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:99688000-99696200	Strong transcription	Fetal Intestine Large	intestine
12	chr7:99688000-99696400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:99688000-99696400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:99688000-99696400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr7:99688000-99696400	Strong transcription	Thymus	Thymus
16	chr7:99688000-99696600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:99688000-99696600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr7:99688000-99696600	Strong transcription	Primary hematopoietic stem cells	blood
19	chr7:99688000-99696600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr7:99688000-99696600	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr7:99688000-99696800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:99688000-99696800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:99688000-99696800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:99688000-99696800	Strong transcription	Brain Angular Gyrus	brain
25	chr7:99688000-99697000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:99688000-99697000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:99688000-99697000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:99688000-99697000	Strong transcription	A549	lung
29	chr7:99688000-99697000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:99688000-99697200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:99688000-99697200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:99688000-99697200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:99688000-99697200	Strong transcription	Brain Anterior Caudate	brain
34	chr7:99688000-99697200	Strong transcription	Brain Hippocampus Middle	brain
35	chr7:99688000-99697200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:99688000-99697200	Strong transcription	Left Ventricle	heart
37	chr7:99688000-99697200	Strong transcription	Ovary	ovary
38	chr7:99688000-99697200	Strong transcription	NHEK	skin
39	chr7:99688200-99695200	Strong transcription	Fetal Lung	lung
40	chr7:99688200-99695400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:99688200-99695800	Strong transcription	Primary T cells from cord blood	blood
42	chr7:99688200-99696200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:99688200-99696200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:99688200-99696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:99688200-99696600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr7:99688200-99696600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr7:99688200-99696600	Strong transcription	Primary B cells from cord blood	blood
48	chr7:99688200-99696600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:99688200-99696600	Strong transcription	Gastric	stomach
50	chr7:99688200-99696600	Strong transcription	Rectal Mucosa Donor 31	rectum

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