Variant report

Variant	rs13148656
Chromosome Location	chr4:57235286-57235287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1042040	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124570	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11538098	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11722404	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723379	0.82[EUR][1000 genomes]
rs11728068	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11732985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11734595	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11937997	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11943048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11946745	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13102012	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs13109030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114481	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13122196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13122422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13122832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13123542	0.91[ASN][1000 genomes]
rs13124065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124696	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs13129188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13131846	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13132553	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13134963	0.85[CEU][hapmap]
rs13135151	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13146014	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13148435	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13150137	0.86[ASN][1000 genomes]
rs13150967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1401908	0.92[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1401911	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2030363	0.84[EUR][1000 genomes]
rs2176785	0.85[CEU][hapmap]
rs3796544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554346	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554347	0.89[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs6554350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811153	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811652	0.84[EUR][1000 genomes]
rs6812222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815480	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818283	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6818340	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6820922	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6823339	0.84[EUR][1000 genomes]
rs6854326	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6857561	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7437329	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7654543	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7656361	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7673373	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682041	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682608	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7695701	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7699157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956275	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995463	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13148656	RPL21P44	cis	cerebellum	SCAN
rs13148656	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13148656	AASDH	cis	multi-tissue	Pritchard
rs13148656	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs13148656	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs13148656	AASDH	cis	parietal	SCAN
rs13148656	AASDH	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
2	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
3	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
5	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
6	chr4:57203200-57251800	Weak transcription	A549	lung
7	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:57204000-57252200	Weak transcription	NH-A	brain
9	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
12	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
15	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
17	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:57213400-57252200	Weak transcription	NHLF	lung
19	chr4:57213600-57250200	Weak transcription	K562	blood
20	chr4:57213600-57252000	Weak transcription	HMEC	breast
21	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:57215000-57238000	Weak transcription	Brain Substantia Nigra	brain
24	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
25	chr4:57216000-57235800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:57216000-57236400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:57216000-57241200	Weak transcription	Pancreas	Pancrea
28	chr4:57216000-57251800	Weak transcription	HepG2	liver
29	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:57216200-57245600	Weak transcription	Colon Smooth Muscle	Colon
32	chr4:57216200-57246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
35	chr4:57218400-57239000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:57218400-57241200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:57219400-57235800	Weak transcription	Left Ventricle	heart
38	chr4:57219400-57236000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:57219800-57236400	Weak transcription	Primary T cells from cord blood	blood
40	chr4:57220400-57235400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr4:57220400-57236000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:57220600-57243400	Weak transcription	HSMM	muscle
43	chr4:57221800-57236000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:57222800-57235800	Weak transcription	Fetal Brain Female	brain
45	chr4:57223000-57235800	Weak transcription	Aorta	Aorta
46	chr4:57223000-57236200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:57223000-57238000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
49	chr4:57223200-57236000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr4:57223200-57253200	Weak transcription	Gastric	stomach

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