Variant report

Variant	rs3024997
Chromosome Location	chr6:43745107-43745108
allele	A/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	chr6:43743876-43745177	PBDE	blood:	n/a	n/a
2	POLR2A	chr6:43737070-43746379	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:43737291-43756474	K562	blood:	n/a	n/a
4	POLR2A	chr6:43736571-43752619	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:43743943-43745432	GM12878	blood:	n/a	n/a
6	HEY1	chr6:43736480-43752618	HepG2	liver:	n/a	chr6:43737671-43737686 chr6:43739793-43739808
7	POLR2A	chr6:43742764-43748019	K562	blood:	n/a	n/a
8	POLR2A	chr6:43745090-43745630	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:43744615-43756551	K562	blood:	n/a	n/a
10	POLR2A	chr6:43738927-43752629	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:43736601-43746456	IMR90	lung:	n/a	n/a
12	POLR2A	chr6:43744707-43745649	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:43744709-43745142	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:43736458-43765400	U87	brain:	n/a	n/a
15	POLR2A	chr6:43736482-43752553	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:43744772-43745737	K562	blood:	n/a	n/a
17	POLR2A	chr6:43737208-43745329	HCT-116	colon:	n/a	n/a
18	POLR2A	chr6:43744645-43746448	K562	blood:	n/a	n/a
19	POLR2A	chr6:43736371-43765427	U87	brain:	n/a	n/a
20	POLR2A	chr6:43744831-43745244	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:43744598-43745301	HepG2	liver:	n/a	n/a
22	POLR2A	chr6:43744602-43752599	K562	blood:	n/a	n/a
23	MAZ	chr6:43735419-43745130	IMR90	lung:	n/a	chr6:43739126-43739135 chr6:43736845-43736855 chr6:43739801-43739811 chr6:43739253-43739262 chr6:43739604-43739614 chr6:43739715-43739724 chr6:43737895-43737904 chr6:43739142-43739151
24	POLR2A	chr6:43736623-43760187	U87	brain:	n/a	n/a
25	CHD1	chr6:43736165-43753887	IMR90	lung:	n/a	chr6:43739796-43739806 chr6:43739318-43739328

No.	Distal block	Cell Line	Cell type
1	chr6:43742782..43745224-chr6:44046035..44049278,3	MCF-7	breast:
2	chr6:43742777..43745112-chr6:43953190..43954729,2	K562	blood:
3	chr6:43736441..43745894-chr6:44037513..44049664,39	K562	blood:
4	chr6:43594866..43599640-chr6:43736940..43745540,22	K562	blood:
5	chr6:43745073..43748024-chr6:44039738..44042379,2	K562	blood:
6	chr6:43653530..43655714-chr6:43743372..43745381,2	K562	blood:

Variant related genes	Relation type
VEGFA	TF binding region
ENSG00000172432	Chromatin interaction
ENSG00000237686	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000096080	Chromatin interaction
ENSG00000231881	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2010963	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3024998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3025000	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs699946	0.86[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs735286	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833060	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs833068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833069	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs865577	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869383	chr6:43505094-43752189	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
3	nsv1018626	chr6:43694649-43803732	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv885848	chr6:43732669-43753051	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3024997	LMO3	trans	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:43740200-43748000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:43740200-43752200	Weak transcription	Aorta	Aorta
3	chr6:43740600-43745400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
4	chr6:43740800-43755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:43742600-43745200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:43742600-43746200	Enhancers	Fetal Heart	heart
7	chr6:43742600-43756400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:43742800-43750200	Genic enhancers	Gastric	stomach
9	chr6:43743000-43745400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:43743000-43745600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:43743000-43745600	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr6:43743000-43746000	Weak transcription	HSMMtube	muscle
13	chr6:43743000-43747200	Genic enhancers	Liver	Liver
14	chr6:43743000-43751000	Genic enhancers	Left Ventricle	heart
15	chr6:43743000-43766400	Weak transcription	HUVEC	blood vessel
16	chr6:43743200-43745200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:43743200-43745200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:43743200-43745200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:43743200-43745200	Weak transcription	Ovary	ovary
20	chr6:43743200-43745400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:43743200-43745600	Genic enhancers	K562	blood
22	chr6:43743200-43745800	Genic enhancers	Fetal Muscle Leg	muscle
23	chr6:43743200-43748800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:43743200-43753600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:43743200-43754600	Strong transcription	Dnd41	blood
26	chr6:43743400-43745200	Weak transcription	Placenta	Placenta
27	chr6:43743400-43745400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:43743400-43745400	Weak transcription	NH-A	brain
29	chr6:43743400-43746200	Weak transcription	Fetal Brain Male	brain
30	chr6:43743400-43753800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:43743400-43754600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:43743400-43754800	Strong transcription	HSMM	muscle
33	chr6:43743600-43745200	Weak transcription	Small Intestine	intestine
34	chr6:43743600-43745400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:43743600-43746400	Strong transcription	Fetal Lung	lung
36	chr6:43743600-43747800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:43743600-43753400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr6:43743600-43753600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:43743600-43753600	Strong transcription	NHEK	skin
40	chr6:43743600-43754000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:43743800-43751200	Genic enhancers	Pancreas	Pancrea
42	chr6:43743800-43753600	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr6:43743800-43753800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:43744000-43745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:43744000-43745200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:43744000-43746000	Weak transcription	Brain Angular Gyrus	brain
47	chr6:43744000-43752200	Genic enhancers	Right Ventricle	heart
48	chr6:43744000-43753600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:43744000-43753800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:43744000-43753800	Strong transcription	Primary monocytes fromperipheralblood	blood

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