Variant report

Variant	rs17045199
Chromosome Location	chr2:53993487-53993488
allele	A/G
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	ZNF143	chr2:53992959-53993546	K562	blood:	n/a	n/a
2	MYC	chr2:53992655-53993520	K562	blood:	n/a	chr2:53993471-53993480 chr2:53992674-53992684
3	CTCF	chr2:53993098-53993625	K562	blood:	n/a	n/a
4	GATA1	chr2:53992640-53993785	PBDE	blood:	n/a	n/a
5	NFYB	chr2:53993338-53993589	Hela-S3	cervix:	n/a	n/a
6	NFYB	chr2:53993285-53993546	GM12878	blood:	n/a	n/a
7	EP300	chr2:53993052-53993545	K562	blood:	n/a	n/a
8	USF1	chr2:53993275-53993592	K562	blood:	n/a	n/a
9	NFYB	chr2:53993269-53993590	K562	blood:	n/a	n/a
10	HCFC1	chr2:53993459-53993788	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53780507..53782864-chr2:53992929..53994536,2	K562	blood:
2	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
CHAC2	TF binding region
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10490468	0.83[CEU][hapmap];0.86[MEX][hapmap]
rs17039525	0.90[ASN][1000 genomes]
rs2253760	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs2542571	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.85[ASN][1000 genomes]
rs2542575	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2542577	0.84[ASN][1000 genomes]
rs2542582	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs2542589	0.83[CEU][hapmap]
rs2542591	0.87[CEU][hapmap]
rs2542592	0.87[CEU][hapmap]
rs2692514	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.88[ASN][1000 genomes]
rs2692516	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692519	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs2692533	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs2692534	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2909261	0.81[ASN][1000 genomes]
rs3095756	0.84[ASN][1000 genomes]
rs35487539	0.89[ASN][1000 genomes]
rs3731970	0.81[ASN][1000 genomes]
rs3770407	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3770408	0.81[ASN][1000 genomes]
rs3770409	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56056250	0.80[EUR][1000 genomes]
rs58359565	0.90[ASN][1000 genomes]
rs60282090	0.87[EUR][1000 genomes]
rs62137566	0.83[ASN][1000 genomes]
rs62139788	0.85[EUR][1000 genomes]
rs698853	0.83[ASN][1000 genomes]
rs698855	0.95[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs7583622	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7600981	0.85[EUR][1000 genomes]
rs766075	0.91[CHB][hapmap]
rs805321	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs805328	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805334	0.81[CEU][hapmap]
rs805351	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs805352	0.95[CHB][hapmap];0.85[MEX][hapmap]
rs805365	0.95[CHB][hapmap];0.85[MEX][hapmap]
rs805386	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs805399	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs805401	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs805404	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs805408	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs805426	0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs805437	0.88[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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17045199	PSME4	cis	lymphoblastoid	seeQTL
rs17045199	ACYP2	cis	multi-tissue	Pritchard
rs17045199	PRDXDD1P	cis	parietal	SCAN
rs17045199	MTIF2	cis	cerebellum	SCAN
rs17045199	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
3	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:53963000-53994000	Weak transcription	A549	lung
8	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
9	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
10	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:53979400-53994000	Weak transcription	Osteobl	bone
12	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
13	chr2:53979800-53994200	Weak transcription	NHLF	lung
14	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
15	chr2:53982800-53994000	Weak transcription	HMEC	breast
16	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine
18	chr2:53984200-53994200	Weak transcription	HSMMtube	muscle
19	chr2:53984200-53994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:53984200-53994400	Weak transcription	Lung	lung
21	chr2:53984200-53994400	Weak transcription	Right Ventricle	heart
22	chr2:53984600-53994400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:53984800-53994200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:53984800-53994400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:53986400-53994000	Weak transcription	Brain Germinal Matrix	brain
26	chr2:53986400-53994000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:53986400-53994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:53987200-53994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:53989800-53994200	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:53990600-53993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:53990800-53994000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:53990800-53994000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:53990800-53994000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:53990800-53994000	Weak transcription	HUVEC	blood vessel
35	chr2:53990800-53994000	Weak transcription	NHEK	skin
36	chr2:53990800-53994200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:53990800-53994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:53990800-53994200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:53990800-53994200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:53990800-53994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:53990800-53994200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:53990800-53994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:53990800-53994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:53990800-53994200	Weak transcription	Adipose Nuclei	Adipose
45	chr2:53990800-53994200	Weak transcription	Brain Anterior Caudate	brain
46	chr2:53990800-53994200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:53990800-53994200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:53990800-53994400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:53990800-53994400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:53990800-53994400	Weak transcription	H9 Cell Line	embryonic stem cell

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