Variant report

Variant	rs3731967
Chromosome Location	chr2:54202448-54202449
allele	A/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	GATA1	chr2:54202417-54203525	PBDE	blood:	n/a	chr2:54202622-54202643 chr2:54203027-54203039 chr2:54203025-54203041 chr2:54202625-54202641

No.	Distal block	Cell Line	Cell type
1	chr2:54074773..54076424-chr2:54200661..54203380,2	MCF-7	breast:
2	chr2:54196505..54198670-chr2:54201640..54204487,2	K562	blood:
3	chr2:54201384..54203059-chr2:55863159..55864990,2	K562	blood:
4	chr2:54198790..54200475-chr2:54201295..54203717,2	K562	blood:

Variant related genes	Relation type
PSME4	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000265452	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10084374	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10167891	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10168293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181999	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10183655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10186566	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11674724	0.87[ASN][1000 genomes]
rs11683741	0.94[ASN][1000 genomes]
rs11689025	0.97[ASN][1000 genomes]
rs11694711	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11890838	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs11893270	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13394278	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477258	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17039547	0.83[CHD][hapmap];0.85[GIH][hapmap]
rs17045452	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.96[ASN][1000 genomes]
rs17045474	0.82[CHB][hapmap]
rs17045488	0.82[CHB][hapmap]
rs1877908	0.83[CHD][hapmap]
rs2112122	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253760	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2542571	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs2542575	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2692514	0.81[CHB][hapmap]
rs2692516	0.83[CHB][hapmap]
rs2692534	0.83[CHB][hapmap]
rs28653587	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28851028	0.84[ASN][1000 genomes]
rs2909459	0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs2949815	0.92[ASN][1000 genomes]
rs34498089	0.85[CHD][hapmap];0.85[GIH][hapmap]
rs4671742	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671746	0.87[ASN][1000 genomes]
rs4671747	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55692047	0.89[ASN][1000 genomes]
rs56302494	0.88[ASN][1000 genomes]
rs62139336	0.96[ASN][1000 genomes]
rs6545377	0.89[ASN][1000 genomes]
rs6545380	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545381	0.81[ASN][1000 genomes]
rs66773232	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6711105	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711217	0.83[EUR][1000 genomes]
rs6714450	0.81[ASN][1000 genomes]
rs6715488	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6742042	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743455	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6748976	0.89[ASN][1000 genomes]
rs6748997	0.87[ASN][1000 genomes]
rs6751105	0.81[CHD][hapmap]
rs698855	0.87[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs72799298	0.89[ASN][1000 genomes]
rs72904908	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559947	0.96[ASN][1000 genomes]
rs7564912	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7591431	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs805309	0.80[CEU][hapmap]
rs805310	0.95[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs805321	0.87[CHB][hapmap]
rs805328	0.90[CHB][hapmap]
rs805344	0.94[ASN][1000 genomes]
rs805351	0.87[CHB][hapmap]
rs805352	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs805365	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs805386	0.87[CHB][hapmap]
rs805399	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs805401	0.87[CHB][hapmap]
rs805404	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs805408	0.87[CHB][hapmap]
rs805416	0.85[AMR][1000 genomes]
rs805426	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs9631059	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3731967	PSME4	cis	lymphoblastoid	seeQTL
rs3731967	ASB3	cis	cerebellum	SCAN
rs3731967	MTIF2	cis	cerebellum	SCAN
rs3731967	TSPYL6	cis	cerebellum	SCAN
rs3731967	RAE1	trans	cerebellum	SCAN
rs3731967	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
3	chr2:54198800-54202600	Weak transcription	Lung	lung
4	chr2:54198800-54204200	Weak transcription	Esophagus	oesophagus
5	chr2:54198800-54205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54199000-54203200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:54199000-54203400	Weak transcription	Left Ventricle	heart
8	chr2:54199000-54203400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:54199000-54204200	Weak transcription	Thymus	Thymus
10	chr2:54199000-54207200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:54199000-54208600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
13	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
17	chr2:54199200-54202800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:54199200-54204200	Weak transcription	Pancreas	Pancrea
19	chr2:54199200-54204400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:54199200-54204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:54199200-54205600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:54199200-54206000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:54199200-54206200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:54199200-54207000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:54199200-54207000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:54199200-54207000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:54199200-54207000	Weak transcription	Fetal Brain Male	brain
28	chr2:54199200-54207200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:54199200-54207400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:54199200-54207600	Weak transcription	Brain Germinal Matrix	brain
31	chr2:54199200-54207600	Weak transcription	Fetal Brain Female	brain
32	chr2:54199200-54207800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:54199200-54208000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:54199200-54209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:54199200-54210600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
37	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
38	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
39	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
40	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
41	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:54199200-54214200	Weak transcription	NH-A	brain
44	chr2:54199200-54214400	Weak transcription	A549	lung
45	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:54199400-54203200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:54199400-54204200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:54199400-54209600	Weak transcription	HSMM	muscle
49	chr2:54199800-54204000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:54200000-54202600	Weak transcription	Brain Anterior Caudate	brain

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