Variant report

Variant	rs2280231
Chromosome Location	chr11:47600438-47600439
allele	C/T
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	chr11:47600066-47600925	GM19099	blood:	n/a	n/a
2	E2F4	chr11:47599970-47600773	K562	blood:	n/a	chr11:47600273-47600284 chr11:47600356-47600365
3	POLR2A	chr11:47600303-47600936	K562	blood:	n/a	n/a
4	IRF1	chr11:47600246-47600833	K562	blood:	n/a	n/a
5	ETS1	chr11:47599981-47600951	K562	blood:	n/a	chr11:47600322-47600333 chr11:47600520-47600530 chr11:47600524-47600533 chr11:47600569-47600578 chr11:47600563-47600572 chr11:47600520-47600531 chr11:47600569-47600578 chr11:47600565-47600572
6	POLR2A	chr11:47600059-47600897	A549	lung:	n/a	n/a
7	POLR2A	chr11:47600015-47601283	K562	blood:	n/a	n/a
8	MXI1	chr11:47600048-47601045	HepG2	liver:	n/a	chr11:47600255-47600270 chr11:47600242-47600257 chr11:47600257-47600272
9	POU2F2	chr11:47600349-47600748	GM12878	blood:	n/a	chr11:47600361-47600373
10	TCF7L2	chr11:47600121-47600961	HCT-116	colon:	n/a	n/a
11	SRF	chr11:47600423-47600684	HepG2	liver:	n/a	n/a
12	ZC3H11A	chr11:47600317-47601001	K562	blood:	n/a	n/a
13	SP1	chr11:47599956-47600949	A549	lung:	n/a	chr11:47600362-47600371 chr11:47600323-47600335 chr11:47600323-47600335 chr11:47600324-47600333 chr11:47600360-47600371 chr11:47600360-47600372 chr11:47600324-47600334 chr11:47600354-47600366 chr11:47600354-47600366 chr11:47600360-47600372 chr11:47600356-47600365
14	JUND	chr11:47600377-47600825	A549	lung:	n/a	n/a
15	TBL1XR1	chr11:47600101-47601049	K562	blood:	n/a	n/a
16	CEBPD	chr11:47600383-47600785	HepG2	liver:	n/a	n/a
17	ELF1	chr11:47600033-47600992	MCF-7	breast:	n/a	chr11:47600523-47600532 chr11:47600521-47600534 chr11:47600522-47600531
18	STAT3	chr11:47600102-47600692	MCF10A-Er-Src	breast:	n/a	chr11:47600325-47600337
19	EGR1	chr11:47600163-47600705	GM12878	blood:	n/a	chr11:47600319-47600332 chr11:47600287-47600297 chr11:47600358-47600368 chr11:47600357-47600370 chr11:47600315-47600337 chr11:47600356-47600371 chr11:47600357-47600370
20	REST	chr11:47600401-47600711	GM12878	blood:	n/a	n/a
21	SIN3AK20	chr11:47599853-47601201	MCF-7	breast:	n/a	n/a
22	POLR2A	chr11:47599987-47600991	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr11:47600350-47600787	PFSK-1	brain:	n/a	n/a
24	MXI1	chr11:47599872-47601023	GM12878	blood:	n/a	chr11:47600255-47600270 chr11:47600242-47600257 chr11:47600257-47600272
25	RAD21	chr11:47600411-47600750	Hela-S3	cervix:	n/a	n/a
26	PML	chr11:47600124-47600793	GM12878	blood:	n/a	chr11:47600403-47600411
27	RAD21	chr11:47599950-47601001	H1-hESC	embryonic stem cell:	n/a	chr11:47600179-47600189
28	PAX5	chr11:47600219-47600927	GM12878	blood:	n/a	chr11:47600717-47600735
29	POLR2A	chr11:47599805-47600926	PANC-1	pancreas:	n/a	n/a
30	FOSL2	chr11:47600294-47600729	A549	lung:	n/a	n/a
31	HDAC2	chr11:47600353-47600845	MCF-7	breast:	n/a	n/a
32	POLR2A	chr11:47599931-47600909	H1-hESC	embryonic stem cell:	n/a	n/a
33	IRF1	chr11:47600239-47600782	K562	blood:	n/a	n/a
34	GABPA	chr11:47600029-47601264	HL-60	blood:	n/a	n/a
35	CUX1	chr11:47600410-47600667	GM12878	blood:	n/a	n/a
36	CTCF	chr11:47600408-47600655	K562	blood:	n/a	n/a
37	REST	chr11:47600245-47600889	PFSK-1	brain:	n/a	n/a
38	BCLAF1	chr11:47600246-47600862	K562	blood:	n/a	chr11:47600522-47600531 chr11:47600563-47600572
39	POLR2A	chr11:47599950-47601044	HL-60	blood:	n/a	n/a
40	SMARCC1	chr11:47599923-47601030	Hela-S3	cervix:	n/a	n/a
41	PAX5	chr11:47600434-47600755	GM12892	blood:	n/a	chr11:47600717-47600735
42	USF1	chr11:47600342-47600664	A549	lung:	n/a	n/a
43	SP1	chr11:47600102-47600787	GM12878	blood:	n/a	chr11:47600362-47600371 chr11:47600323-47600335 chr11:47600323-47600335 chr11:47600324-47600333 chr11:47600360-47600371 chr11:47600360-47600372 chr11:47600324-47600334 chr11:47600354-47600366 chr11:47600354-47600366 chr11:47600360-47600372 chr11:47600356-47600365
44	POLR2A	chr11:47598947-47601303	HepG2	liver:	n/a	n/a
45	SMC3	chr11:47600432-47600701	K562	blood:	n/a	n/a
46	NFIC	chr11:47600242-47600820	HepG2	liver:	n/a	n/a
47	RELA	chr11:47600206-47600789	GM19099	blood:	n/a	n/a
48	REST	chr11:47600359-47600825	Hela-S3	cervix:	n/a	n/a
49	GABPA	chr11:47599842-47601517	A549	lung:	n/a	n/a
50	RAD21	chr11:47600135-47600862	H1-hESC	embryonic stem cell:	n/a	chr11:47600179-47600189

No.	Distal block	Cell Line	Cell type
1	chr11:47572291..47576392-chr11:47598056..47603377,7	K562	blood:
2	chr11:47574450..47575951-chr11:47599292..47600981,2	MCF-7	breast:
3	chr11:47600406..47601156-chr2:131113338..131114099,2	Hela-S3	cervix:
4	chr11:47599594..47601938-chr11:47869864..47871887,2	K562	blood:
5	chr11:47597275..47600063-chr11:47600255..47602444,2	MCF-7	breast:
6	chr11:47599184..47601918-chr11:47661794..47664226,4	MCF-7	breast:
7	chr11:47597915..47601799-chr11:47868286..47871887,4	K562	blood:
8	chr11:47585423..47588969-chr11:47597747..47604797,13	K562	blood:
9	chr11:47426650..47429548-chr11:47599829..47602825,2	MCF-7	breast:
10	chr11:47572538..47574748-chr11:47599210..47602112,3	MCF-7	breast:
11	chr11:47599811..47601393-chr11:47661829..47664063,2	K562	blood:

Variant related genes	Relation type
NDUFS3	TF binding region
RNU5E-10P	TF binding region
KBTBD4	TF binding region
ENSG00000231880	Chromatin interaction
ENSG00000072135	Chromatin interaction
ENSG00000200376	Chromatin interaction
ENSG00000110536	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000109919	Chromatin interaction
ENSG00000213619	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1017730	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs10769288	0.87[JPT][hapmap]
rs10838703	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap]
rs10838726	0.91[CEU][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10838731	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11039266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes]
rs11039284	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039290	0.91[CEU][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11039297	0.85[EUR][1000 genomes]
rs11039332	0.82[CEU][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap]
rs11606287	0.85[CHB][hapmap];0.87[CHD][hapmap];0.87[MEX][hapmap]
rs12224672	0.83[AMR][1000 genomes]
rs12225051	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361415	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs12577643	0.88[CEU][hapmap]
rs2293576	1.00[ASW][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs61895112	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6485758	0.91[CEU][hapmap]
rs7103835	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7118178	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120548	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs71475921	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7927445	0.82[CEU][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs7933019	0.91[CEU][hapmap]

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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv314	chr11:47561564-47606256	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2280231	MTCH2	cis	cerebellum	SCAN
rs2280231	MADD	cis	parietal	SCAN
rs2280231	C1QTNF4	cis	lymphoblastoid	seeQTL
rs2280231	C1QTNF4	cis	multi-tissue	Pritchard
rs2280231	ACCSL	cis	parietal	SCAN
rs2280231	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47599000-47601200	Active TSS	Fetal Kidney	kidney
2	chr11:47599600-47601600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr11:47599600-47601800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr11:47599800-47600600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:47599800-47601000	Active TSS	Brain Angular Gyrus	brain
6	chr11:47599800-47601000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:47599800-47601000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr11:47599800-47601000	Active TSS	Placenta Amnion	Placenta Amnion
9	chr11:47599800-47601000	Transcr. at gene 5' and 3'	Right Atrium	heart
10	chr11:47599800-47601000	Active TSS	NHLF	lung
11	chr11:47599800-47601200	Active TSS	Muscle Satellite Cultured Cells	--
12	chr11:47599800-47601200	Active TSS	Aorta	Aorta
13	chr11:47599800-47601200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr11:47599800-47601200	Active TSS	Fetal Brain Female	brain
15	chr11:47599800-47601400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr11:47599800-47601400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr11:47599800-47601400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47599800-47601400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:47599800-47601400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:47599800-47601400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:47599800-47601400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:47599800-47601400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:47599800-47601400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:47599800-47601400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:47599800-47601400	Active TSS	Lung	lung
26	chr11:47599800-47601400	Active TSS	Ovary	ovary
27	chr11:47599800-47601400	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr11:47599800-47601400	Active TSS	Small Intestine	intestine
29	chr11:47599800-47601400	Active TSS	HSMM	muscle
30	chr11:47599800-47601400	Active TSS	NHDF-Ad	bronchial
31	chr11:47599800-47601600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr11:47599800-47601600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:47599800-47601600	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr11:47599800-47601600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:47599800-47601600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:47599800-47601600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:47599800-47601600	Active TSS	Gastric	stomach
38	chr11:47599800-47601800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr11:47599800-47601800	Active TSS	Left Ventricle	heart
40	chr11:47599800-47601800	Active TSS	Right Ventricle	heart
41	chr11:47599800-47602000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr11:47599800-47602000	Active TSS	Psoas Muscle	Psoas
43	chr11:47600000-47600800	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr11:47600000-47600800	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr11:47600000-47600800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr11:47600000-47600800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:47600000-47600800	Active TSS	Fetal Lung	lung
48	chr11:47600000-47600800	Active TSS	Spleen	Spleen
49	chr11:47600000-47601000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:47600000-47601000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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