Variant report

Variant	rs9887904
Chromosome Location	chr1:158978596-158978597
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	chr1:158978406-158980376	GM12892	blood:	n/a	n/a
2	TBP	chr1:158978436-158980668	GM12878	blood:	n/a	n/a
3	PAX5	chr1:158978546-158978943	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:158978455-158980617	GM18951	blood:	n/a	n/a
5	POU2F2	chr1:158978568-158978942	GM12878	blood:	n/a	n/a
6	RFX5	chr1:158978452-158978790	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:158978428-158980356	GM12892	blood:	n/a	n/a
8	KAP1	chr1:158978548-158980551	HEK293	kidney:	n/a	chr1:158979354-158979363
9	YY1	chr1:158978531-158980036	GM12878	blood:	n/a	chr1:158979303-158979311
10	PAX5	chr1:158978495-158979011	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:158978508-158980689	GM12892	blood:	n/a	n/a
12	EP300	chr1:158978552-158979260	GM12878	blood:	n/a	chr1:158978888-158978895
13	POLR2A	chr1:158978461-158980586	GM18526	blood:	n/a	n/a
14	NFIC	chr1:158978400-158978964	GM12878	blood:	n/a	n/a
15	RELA	chr1:158978511-158979901	GM19099	blood:	n/a	chr1:158979114-158979123 chr1:158979114-158979123
16	STAT3	chr1:158978239-158978890	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:158978459-158981042	GM15510	blood:	n/a	n/a
18	KAP1	chr1:158978346-158980205	U2OS	brain:	n/a	chr1:158979354-158979363
19	RCOR1	chr1:158978512-158980241	GM12878	blood:	n/a	n/a
20	ATF2	chr1:158978470-158978975	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:158978512-158979059	GM12891	blood:	n/a	n/a
22	MAZ	chr1:158978304-158979927	GM12878	blood:	n/a	n/a
23	YY1	chr1:158978538-158978943	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:158978457-158980760	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
26	CHD2	chr1:158978435-158980163	GM12878	blood:	n/a	n/a
27	SP1	chr1:158978450-158978950	GM12878	blood:	n/a	chr1:158978705-158978712
28	SIN3A	chr1:158978500-158978951	GM12878	blood:	n/a	n/a
29	POU2F2	chr1:158978579-158978962	GM12891	blood:	n/a	n/a
30	SP1	chr1:158978453-158978962	GM12878	blood:	n/a	chr1:158978705-158978712
31	CHD1	chr1:158978577-158980909	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:158978242-158981066	GM12878	blood:	n/a	n/a
33	MAX	chr1:158978591-158979010	NB4	blood:	n/a	n/a
34	POLR2A	chr1:158978498-158979051	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:158978391-158981364	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:158978592-158978985	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:158978442-158980954	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:158978595-158980199	GM12878	blood:	n/a	n/a
39	FOXM1	chr1:158978448-158978927	GM12878	blood:	n/a	n/a
40	PML	chr1:158978434-158980352	GM12878	blood:	n/a	chr1:158979354-158979363
41	YY1	chr1:158978590-158978958	GM12891	blood:	n/a	n/a
42	ETS1	chr1:158978470-158978937	GM12878	blood:	n/a	chr1:158978887-158978896 chr1:158978887-158978896 chr1:158978887-158978896 chr1:158978884-158978897 chr1:158978887-158978896 chr1:158978887-158978896 chr1:158978887-158978898 chr1:158978887-158978896 chr1:158978883-158978899
43	EBF1	chr1:158978563-158979266	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
45	TAF1	chr1:158978590-158978956	GM12891	blood:	n/a	n/a
46	TAF1	chr1:158978478-158979031	GM12878	blood:	n/a	n/a
47	EP300	chr1:158978501-158979039	GM12878	blood:	n/a	chr1:158978888-158978895 chr1:158978533-158978547
48	WRNIP1	chr1:158978264-158980226	GM12878	blood:	n/a	n/a
49	BCLAF1	chr1:158978480-158978976	GM12878	blood:	n/a	chr1:158978887-158978896
50	RUNX3	chr1:158978449-158979014	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158900682..158902203-chr1:158976628..158979178,2	K562	blood:
2	chr1:158978448..158981430-chr1:159044743..159047016,2	K562	blood:

Variant related genes	Relation type
IFI16	TF binding region
ENSG00000163564	Chromatin interaction
ENSG00000163568	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11578363	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11583269	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12071289	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1614568	0.85[CEU][hapmap]
rs1623601	0.86[CEU][hapmap];0.86[MEX][hapmap]
rs56039305	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56050841	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56317833	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60594681	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72704962	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs860635	0.82[AMR][1000 genomes];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	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9887904	NUP210L	cis	parietal	SCAN
rs9887904	S100A8	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158970000-158978600	Weak transcription	Esophagus	oesophagus
2	chr1:158970200-158978600	Weak transcription	Psoas Muscle	Psoas
3	chr1:158970200-158978800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:158970200-158979200	Weak transcription	Aorta	Aorta
5	chr1:158970800-158980800	Weak transcription	Pancreas	Pancrea
6	chr1:158971200-158978600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:158971200-158978600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:158971200-158978800	Weak transcription	HSMMtube	muscle
9	chr1:158971800-158978600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:158971800-158979800	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:158972000-158979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:158975000-158978800	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:158975000-158979800	Weak transcription	Lung	lung
14	chr1:158975400-158978600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:158975400-158979200	Weak transcription	Liver	Liver
16	chr1:158975400-158979200	Weak transcription	Right Atrium	heart
17	chr1:158975800-158978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:158975800-158978600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:158975800-158978600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:158975800-158979200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:158976000-158978600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:158976000-158978600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:158976000-158979000	Weak transcription	Fetal Stomach	stomach
24	chr1:158976000-158979200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:158976000-158979200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:158976000-158979400	Weak transcription	Left Ventricle	heart
27	chr1:158976000-158979400	Weak transcription	Ovary	ovary
28	chr1:158976000-158979600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:158976000-158983000	Weak transcription	Spleen	Spleen
30	chr1:158976000-159000800	Weak transcription	Gastric	stomach
31	chr1:158976400-158979400	Weak transcription	Fetal Kidney	kidney
32	chr1:158976400-158979400	Weak transcription	Placenta	Placenta
33	chr1:158976400-158979800	Weak transcription	Stomach Mucosa	stomach
34	chr1:158976600-158978800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:158976800-158978800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:158977000-158978800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:158977000-158978800	Enhancers	Primary T cells from cord blood	blood
38	chr1:158977000-158978800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:158977200-158979200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:158977200-158979600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:158977400-158978600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:158977400-158978600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:158977400-158978800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:158977600-158978600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr1:158977600-158978600	Weak transcription	Small Intestine	intestine
47	chr1:158977600-158979400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:158977600-158979600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:158977800-158979600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:158977800-158982400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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