Variant report

Variant	rs2248020
Chromosome Location	chr11:93259965-93259966
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	MTA3	chr11:93258602-93260862	GM12878	blood:	n/a	n/a
2	IKZF1	chr11:93258745-93260241	GM12878	blood:	n/a	n/a
3	RUNX3	chr11:93258735-93260857	GM12878	blood:	n/a	n/a
4	TEAD4	chr11:93259851-93260261	HepG2	liver:	n/a	n/a
5	BCLAF1	chr11:93259221-93260223	GM12878	blood:	n/a	n/a
6	BHLHE40	chr11:93258823-93260678	GM12878	blood:	n/a	chr11:93260246-93260262
7	SPI1	chr11:93259097-93260499	GM12878	blood:	n/a	n/a
8	SPI1	chr11:93259701-93260171	GM12891	blood:	n/a	n/a
9	PML	chr11:93258637-93260716	GM12878	blood:	n/a	chr11:93259037-93259046
10	ATF2	chr11:93258703-93260799	GM12878	blood:	n/a	n/a
11	STAT5A	chr11:93259710-93260669	GM12878	blood:	n/a	n/a
12	MAFK	chr11:93259807-93260200	HepG2	liver:	n/a	n/a
13	SPI1	chr11:93259733-93260165	GM12878	blood:	n/a	n/a
14	FOXM1	chr11:93258823-93260129	GM12878	blood:	n/a	n/a
15	EBF1	chr11:93258987-93260745	GM12878	blood:	n/a	chr11:93259380-93259391
16	POLR2A	chr11:93259501-93260611	GM12878	blood:	n/a	n/a
17	SPI1	chr11:93259724-93260217	HL-60	blood:	n/a	n/a
18	NFIC	chr11:93258744-93260146	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:93259479-93260912	GM12878	blood:	n/a	n/a
20	MTA3	chr11:93259574-93260490	GM12878	blood:	n/a	n/a
21	PAX5	chr11:93259072-93260542	GM12878	blood:	n/a	chr11:93259416-93259434
22	MAFK	chr11:93259862-93260046	HepG2	liver:	n/a	n/a
23	YY1	chr11:93259639-93260140	GM12878	blood:	n/a	n/a
24	EP300	chr11:93259293-93260726	GM12878	blood:	n/a	chr11:93259735-93259749 chr11:93259467-93259481
25	RXRA	chr11:93259914-93260260	HepG2	liver:	n/a	n/a
26	ZNF384	chr11:93258896-93259988	GM12878	blood:	n/a	n/a
27	MAZ	chr11:93259247-93260603	GM12878	blood:	n/a	n/a
28	RUNX3	chr11:93258732-93260827	GM12878	blood:	n/a	n/a
29	SPI1	chr11:93259871-93260084	K562	blood:	n/a	n/a
30	SPI1	chr11:93259834-93260089	GM12878	blood:	n/a	n/a
31	WRNIP1	chr11:93259577-93260920	GM12878	blood:	n/a	n/a
32	TBP	chr11:93259432-93260596	GM12878	blood:	n/a	n/a
33	BCLAF1	chr11:93258713-93260120	GM12878	blood:	n/a	n/a
34	EP300	chr11:93258843-93260664	GM12878	blood:	n/a	chr11:93259735-93259749 chr11:93259467-93259481
35	NFIC	chr11:93258725-93259991	GM12878	blood:	n/a	n/a
36	SPI1	chr11:93259781-93260103	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93259393..93261836-chr11:93266533..93269346,3	K562	blood:
2	chr11:93257690..93261836-chr11:93263663..93269980,6	K562	blood:

Variant related genes	Relation type
SMCO4	TF binding region
ENSG00000234106	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10466368	0.82[EUR][1000 genomes]
rs11601056	0.82[EUR][1000 genomes]
rs11604909	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs1563445	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes]
rs2243410	0.93[EUR][1000 genomes]
rs2248524	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2248531	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2248655	0.96[EUR][1000 genomes]
rs2605611	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2605614	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2605615	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2605617	0.90[EUR][1000 genomes]
rs2605620	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2605622	0.93[EUR][1000 genomes]
rs2605623	0.93[EUR][1000 genomes]
rs2605626	1.00[CEU][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs2605627	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2605628	0.90[EUR][1000 genomes]
rs2605629	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs2658766	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2658767	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2658768	0.97[EUR][1000 genomes]
rs2658769	0.98[EUR][1000 genomes]
rs2658770	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7116173	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2248020	CHORDC1	cis	parietal	SCAN
rs2248020	MTNR1B	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93248000-93261800	Weak transcription	Fetal Stomach	stomach
2	chr11:93249000-93261600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr11:93251000-93261400	Weak transcription	Fetal Brain Male	brain
4	chr11:93251000-93261600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:93251000-93261600	Weak transcription	Aorta	Aorta
6	chr11:93252000-93266800	Enhancers	Fetal Thymus	thymus
7	chr11:93252200-93260800	Enhancers	Dnd41	blood
8	chr11:93253800-93266200	Weak transcription	Fetal Brain Female	brain
9	chr11:93255000-93263600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:93255000-93274600	Weak transcription	Hela-S3	cervix
11	chr11:93255600-93262200	Weak transcription	Brain Germinal Matrix	brain
12	chr11:93255800-93261600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:93255800-93262000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:93255800-93263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:93256000-93262200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:93256200-93263800	Enhancers	Primary B cells from peripheral blood	blood
17	chr11:93256200-93266000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr11:93256400-93266600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:93256800-93261000	Flanking Active TSS	GM12878-XiMat	blood
20	chr11:93257000-93261000	Enhancers	Thymus	Thymus
21	chr11:93257200-93260400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:93257200-93264800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:93257400-93260400	Enhancers	Left Ventricle	heart
24	chr11:93257400-93260600	Enhancers	Fetal Intestine Large	intestine
25	chr11:93257400-93260800	Enhancers	Primary hematopoietic stem cells	blood
26	chr11:93257400-93264000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:93257400-93264800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:93257400-93266600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr11:93257600-93260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:93257600-93260600	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:93257600-93260600	Enhancers	Fetal Intestine Small	intestine
32	chr11:93257600-93260600	Enhancers	Stomach Mucosa	stomach
33	chr11:93257600-93261000	Enhancers	Placenta	Placenta
34	chr11:93257600-93261000	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr11:93257600-93263000	Enhancers	HepG2	liver
36	chr11:93257600-93264000	Enhancers	Right Ventricle	heart
37	chr11:93257600-93264400	Enhancers	Fetal Muscle Leg	muscle
38	chr11:93257800-93260400	Enhancers	Pancreas	Pancrea
39	chr11:93257800-93260400	Enhancers	Right Atrium	heart
40	chr11:93257800-93261000	Enhancers	Psoas Muscle	Psoas
41	chr11:93257800-93261600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr11:93257800-93264200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:93257800-93264200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr11:93258000-93260000	Weak transcription	Lung	lung
45	chr11:93258000-93260600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:93258000-93262400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr11:93258000-93264600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:93258200-93260400	Enhancers	Brain Substantia Nigra	brain
49	chr11:93258200-93262000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:93258200-93266400	Enhancers	Primary T cells from cord blood	blood

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