Variant report

Variant	rs861575
Chromosome Location	chr1:184725099-184725100
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	MXI1	chr1:184722533-184725625	SK-N-SH	brain:	n/a	chr1:184724823-184724832
2	CBX3	chr1:184723113-184725259	K562	blood:	n/a	n/a
3	RUNX3	chr1:184722691-184725219	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:184723000-184725204	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:184724521-184725111	MCF10A-Er-Src	breast:	n/a	n/a
6	TBL1XR1	chr1:184723926-184725319	K562	blood:	n/a	n/a
7	WRNIP1	chr1:184724030-184725142	GM12878	blood:	n/a	n/a
8	RUNX3	chr1:184723077-184725165	GM12878	blood:	n/a	n/a
9	TEAD4	chr1:184722594-184725182	K562	blood:	n/a	n/a
10	MAX	chr1:184723192-184725151	GM12878	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
11	IRF1	chr1:184723783-184725126	K562	blood:	n/a	chr1:184724451-184724460
12	ZMIZ1	chr1:184722820-184725128	K562	blood:	n/a	n/a
13	TBP	chr1:184723164-184725174	K562	blood:	n/a	n/a
14	POLR2A	chr1:184720851-184725115	GM12891	blood:	n/a	n/a
15	POLR2A	chr1:184723208-184725107	K562	blood:	n/a	n/a
16	ARID3A	chr1:184723938-184725344	K562	blood:	n/a	n/a
17	E2F6	chr1:184723192-184725195	K562	blood:	n/a	chr1:184723910-184723918
18	POLR2A	chr1:184723137-184725117	K562	blood:	n/a	n/a
19	MAFK	chr1:184723610-184725116	K562	blood:	n/a	n/a
20	USF2	chr1:184723959-184725241	GM12878	blood:	n/a	n/a
21	GTF2B	chr1:184723807-184725173	K562	blood:	n/a	n/a
22	MYC	chr1:184722796-184725182	K562	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
23	KAP1	chr1:184723201-184725152	HEK293	kidney:	n/a	chr1:184724981-184724989
24	EP300	chr1:184723894-184725153	GM12878	blood:	n/a	chr1:184724971-184724978 chr1:184724045-184724052
25	POLR2A	chr1:184721793-184725128	GM12878	blood:	n/a	n/a
26	BHLHE40	chr1:184723112-184725155	K562	blood:	n/a	n/a
27	EP300	chr1:184723829-184725115	GM12878	blood:	n/a	chr1:184724971-184724978 chr1:184724045-184724052
28	MYC	chr1:184723058-184725294	MCF10A-Er-Src	breast:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
29	CUX1	chr1:184723849-184725665	K562	blood:	n/a	n/a
30	ATF1	chr1:184723843-184725135	K562	blood:	n/a	n/a
31	RCOR1	chr1:184723198-184725102	GM12878	blood:	n/a	n/a
32	MAX	chr1:184723091-184725139	K562	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
33	KAP1	chr1:184724019-184725214	U2OS	brain:	n/a	chr1:184724981-184724989
34	RELA	chr1:184723637-184725117	GM18505	blood:	n/a	n/a
35	CHD2	chr1:184723139-184725144	GM12878	blood:	n/a	n/a
36	MYC	chr1:184723981-184725266	MCF10A-Er-Src	breast:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
37	FOS	chr1:184724434-184725206	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr1:184723133-184725222	K562	blood:	n/a	n/a
39	MYC	chr1:184722796-184725273	K562	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
40	JUND	chr1:184722610-184725155	K562	blood:	n/a	chr1:184723197-184723206
41	MXI1	chr1:184722717-184725127	GM12878	blood:	n/a	chr1:184724823-184724832
42	TAL1	chr1:184723592-184725148	K562	blood:	n/a	chr1:184724445-184724463
43	EP300	chr1:184722721-184725187	K562	blood:	n/a	chr1:184724971-184724978 chr1:184724045-184724052 chr1:184723448-184723457
44	MAX	chr1:184723200-184725116	K562	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
45	POLR2A	chr1:184723161-184725125	K562	blood:	n/a	n/a
46	SMARCC1	chr1:184723143-184725172	Hela-S3	cervix:	n/a	n/a
47	MAX	chr1:184723015-184725207	SK-N-SH	brain:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
48	MYC	chr1:184722739-184725204	K562	blood:	n/a	chr1:184724820-184724835 chr1:184724822-184724832 chr1:184724820-184724830 chr1:184724823-184724830 chr1:184724818-184724833 chr1:184724821-184724832 chr1:184724822-184724831
49	TBP	chr1:184723821-184725182	Hela-S3	cervix:	n/a	n/a
50	MXI1	chr1:184722563-184725346	IMR90	lung:	n/a	chr1:184724823-184724832

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184722993..184726139-chr1:185013897..185016469,4	K562	blood:

Variant related genes	Relation type
EDEM3	TF binding region
ENSG00000121481	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1040666	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1046239	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1061508	0.80[GIH][hapmap]
rs1062994	0.81[EUR][1000 genomes]
rs10752941	0.87[ASN][1000 genomes]
rs10911633	0.81[EUR][1000 genomes]
rs10911634	0.82[EUR][1000 genomes]
rs10911636	0.82[EUR][1000 genomes]
rs10911640	0.84[ASN][1000 genomes]
rs10911644	0.87[CEU][hapmap];0.81[GIH][hapmap];0.83[EUR][1000 genomes]
rs10911645	0.84[EUR][1000 genomes]
rs11808675	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12031028	0.84[EUR][1000 genomes]
rs12043236	0.86[ASN][1000 genomes]
rs12071631	0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12124929	0.83[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs12126231	0.82[EUR][1000 genomes]
rs12131285	0.83[CEU][hapmap]
rs12133128	0.84[EUR][1000 genomes]
rs12184284	0.81[EUR][1000 genomes]
rs12567225	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs12567226	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2024765	0.81[ASN][1000 genomes]
rs2024767	0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2064605	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2207733	0.86[ASN][1000 genomes]
rs2333715	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs2333716	0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3736757	0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3895196	0.94[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4469687	0.86[ASN][1000 genomes]
rs4651230	0.87[CEU][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs6663178	0.94[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6677073	0.84[ASN][1000 genomes]
rs67359172	0.84[EUR][1000 genomes]
rs7523023	0.86[ASN][1000 genomes]
rs7525074	0.86[ASN][1000 genomes]
rs861576	0.90[EUR][1000 genomes]
rs861577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861578	0.84[GIH][hapmap]
rs861579	0.92[ASN][1000 genomes]
rs861581	0.84[GIH][hapmap]
rs861582	0.93[ASN][1000 genomes]
rs861583	0.89[EUR][1000 genomes]
rs9425339	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9425341	0.81[ASN][1000 genomes]
rs9425343	0.87[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs9425633	0.84[ASN][1000 genomes]
rs9658937	0.84[ASN][1000 genomes]
rs9661314	0.84[ASN][1000 genomes]
rs971081	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv3403637	chr1:184722554-184725102	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs861575	PRG4	cis	parietal	SCAN
rs861575	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs861575	EDEM3	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184721800-184725200	Active TSS	Psoas Muscle	Psoas
2	chr1:184721800-184725200	Active TSS	Stomach Mucosa	stomach
3	chr1:184722200-184725200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:184722200-184725200	Active TSS	Fetal Stomach	stomach
5	chr1:184722200-184725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:184722600-184725200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:184722600-184725200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:184722600-184725200	Active TSS	Colonic Mucosa	Colon
9	chr1:184722600-184725200	Active TSS	Right Ventricle	heart
10	chr1:184722600-184725400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:184722800-184725200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:184722800-184725200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:184722800-184725200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:184722800-184725200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:184723000-184725200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:184723000-184725200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:184723000-184725200	Active TSS	Brain Angular Gyrus	brain
18	chr1:184723000-184725200	Active TSS	Placenta	Placenta
19	chr1:184723000-184725200	Active TSS	Rectal Smooth Muscle	rectum
20	chr1:184723000-184725400	Active TSS	Brain Anterior Caudate	brain
21	chr1:184723000-184725400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr1:184723000-184725400	Active TSS	A549	lung
23	chr1:184723200-184725200	Active TSS	Brain Germinal Matrix	brain
24	chr1:184723400-184725200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:184724400-184725200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr1:184724400-184725200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:184724400-184725200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr1:184724400-184725200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:184724400-184725200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:184724400-184725200	Flanking Active TSS	Liver	Liver
31	chr1:184724400-184725200	Flanking Active TSS	Fetal Thymus	thymus
32	chr1:184724400-184725400	Flanking Active TSS	Osteobl	bone
33	chr1:184724600-184725200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:184724600-184725200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:184724600-184725200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:184724600-184725200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr1:184724600-184725200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr1:184724600-184725200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:184724600-184725200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:184724600-184725200	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr1:184724600-184725200	Active TSS	Right Atrium	heart
42	chr1:184724600-184725200	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr1:184724600-184725200	Flanking Active TSS	Hela-S3	cervix
44	chr1:184724600-184725200	Flanking Active TSS	HUVEC	blood vessel
45	chr1:184724600-184725200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:184724600-184725400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:184724600-184725400	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr1:184724600-184725400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr1:184724600-184725400	Flanking Active TSS	Dnd41	blood
50	chr1:184724600-184725400	Flanking Active TSS	HMEC	breast

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