Variant report

Variant	rs3824999
Chromosome Location	chr11:74345550-74345551
allele	A/C
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	chr11:74345436-74345784	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr11:74345508-74346006	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr11:74345262-74346307	A549	lung:	n/a	chr11:74345841-74345859 chr11:74345842-74345858 chr11:74345843-74345864
4	MAFF	chr11:74345532-74345834	K562	blood:	n/a	n/a
5	NFIC	chr11:74345434-74345981	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr11:74345528-74346169	MCF-7	breast:	n/a	chr11:74345842-74345861
7	CTCF	chr11:74345540-74345690	HFF-Myc	foreskin:	n/a	n/a
8	NFIC	chr11:74345449-74346007	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr11:74345495-74345911	HCT-116	colon:	n/a	n/a
10	KAP1	chr11:74345547-74346024	U2OS	brain:	n/a	n/a
11	MYC	chr11:74345531-74346029	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr11:74345504-74345864	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr11:74345501-74345892	K562	blood:	n/a	n/a
14	NFIC	chr11:74345336-74346076	ECC-1	luminal epithelium:	n/a	n/a
15	SP1	chr11:74345391-74346055	A549	lung:	n/a	n/a
16	MXI1	chr11:74345523-74345661	K562	blood:	n/a	n/a
17	RAD21	chr11:74345473-74346141	MCF-7	breast:	n/a	chr11:74345842-74345861
18	MAFK	chr11:74345537-74345903	K562	blood:	n/a	n/a
19	FOSL2	chr11:74345405-74345958	A549	lung:	n/a	n/a
20	FOS	chr11:74345480-74346014	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr11:74345133-74345988	MCF10A-Er-Src	breast:	n/a	n/a
22	RAD21	chr11:74345516-74346181	HCT-116	colon:	n/a	chr11:74345842-74345861
23	RAD21	chr11:74345406-74346255	SK-N-SH	brain:	n/a	chr11:74345842-74345861
24	FOS	chr11:74345481-74345853	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr11:74345510-74345843	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr11:74345481-74346163	SK-N-SH	brain:	n/a	chr11:74345841-74345859 chr11:74345842-74345858 chr11:74345843-74345864
27	RAD21	chr11:74345537-74346038	A549	lung:	n/a	chr11:74345842-74345861
28	JUND	chr11:74345474-74345980	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:74345519..74346061-chr11:74413099..74414091,2	K562	blood:
2	chr11:74339791..74343200-chr11:74343975..74347157,5	MCF-7	breast:
3	chr11:74333645..74336411-chr11:74344978..74348426,3	K562	blood:
4	chr11:74345263..74346988-chr11:74412818..74415063,2	MCF-7	breast:
5	chr11:74345364..74346309-chr11:74437358..74438299,9	MCF-7	breast:
6	chr11:74343993..74348455-chr11:74350438..74354140,4	K562	blood:
7	chr11:74345424..74346152-chr11:74437689..74438208,2	MCF-7	breast:
8	chr11:74343839..74346032-chr11:74354471..74356643,2	K562	blood:
9	chr11:74345344..74346333-chr11:74437377..74438211,2	K562	blood:
10	chr11:74333645..74336229-chr11:74343900..74348454,4	K562	blood:

Variant related genes	Relation type
POLD3	TF binding region
ENSG00000077514	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10219203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793092	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs10793093	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10793094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793098	0.88[ASN][1000 genomes]
rs10793101	0.84[EUR][1000 genomes]
rs10899009	0.83[ASN][1000 genomes]
rs10899020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899024	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10899029	0.84[EUR][1000 genomes]
rs11236158	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11236161	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236164	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236178	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236182	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236189	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236199	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11236200	0.85[EUR][1000 genomes]
rs11604752	0.83[ASN][1000 genomes]
rs11825804	0.84[EUR][1000 genomes]
rs12282266	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421429	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1944933	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117222	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4420291	0.84[EUR][1000 genomes]
rs4644667	0.91[ASN][1000 genomes]
rs57796856	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58659624	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59830047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60085010	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103197	0.92[ASN][1000 genomes]
rs7109940	0.84[EUR][1000 genomes]
rs7121958	0.85[ASN][1000 genomes]
rs7124188	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72977282	0.94[ASN][1000 genomes]
rs7924706	0.98[ASN][1000 genomes]
rs7932922	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7937753	0.98[ASN][1000 genomes]
rs7940880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Colorectal cancer	22634755	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3824999	RNF121	cis	cerebellum	SCAN
rs3824999	ARHGEF17	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74304400-74345600	Weak transcription	Gastric	stomach
2	chr11:74304600-74345600	Weak transcription	Esophagus	oesophagus
3	chr11:74304600-74373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:74304800-74357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:74304800-74361400	Weak transcription	Colonic Mucosa	Colon
6	chr11:74310200-74352400	Weak transcription	Fetal Brain Male	brain
7	chr11:74314000-74370200	Weak transcription	Psoas Muscle	Psoas
8	chr11:74317200-74345600	Weak transcription	Pancreas	Pancrea
9	chr11:74317200-74352200	Weak transcription	Aorta	Aorta
10	chr11:74319200-74366000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr11:74321600-74364800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:74322200-74357400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:74323000-74356800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:74324000-74345600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:74324200-74345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:74324400-74346600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:74325000-74345600	Weak transcription	Spleen	Spleen
18	chr11:74325000-74346400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:74325000-74351600	Weak transcription	Right Ventricle	heart
20	chr11:74325200-74347000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:74325200-74351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:74325400-74345600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr11:74325400-74346200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:74325600-74350600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:74328400-74345600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:74329800-74346400	Weak transcription	Fetal Intestine Small	intestine
27	chr11:74330000-74345600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:74330200-74345600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:74330200-74346200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:74330200-74351600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:74331200-74345600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:74331400-74346000	Weak transcription	HepG2	liver
33	chr11:74331400-74383400	Weak transcription	Brain Substantia Nigra	brain
34	chr11:74331600-74345600	Weak transcription	Liver	Liver
35	chr11:74331600-74346200	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:74331800-74345600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:74332200-74345800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr11:74332200-74348800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:74332400-74345600	Weak transcription	Brain Germinal Matrix	brain
40	chr11:74332400-74345800	Weak transcription	Lung	lung
41	chr11:74332400-74346600	Weak transcription	Ovary	ovary
42	chr11:74332800-74345600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:74332800-74345600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:74332800-74345600	Weak transcription	Thymus	Thymus
45	chr11:74332800-74345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:74332800-74345800	Weak transcription	Brain Anterior Caudate	brain
47	chr11:74335200-74356800	Strong transcription	Fetal Thymus	thymus
48	chr11:74335200-74357000	Strong transcription	Dnd41	blood
49	chr11:74336000-74354400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:74336200-74358200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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