Variant report

Variant	rs13141793
Chromosome Location	chr4:57247862-57247863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57244769..57248876-chr4:57249914..57255164,10	K562	blood:
2	chr4:57247026..57248571-chr4:57274009..57276272,2	K562	blood:
3	chr4:57245776..57248590-chr4:57250681..57253317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000269921	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10031012	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10031550	0.86[EUR][1000 genomes]
rs11133438	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11133439	0.81[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610	0.91[JPT][hapmap]
rs11724302	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733474	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs12646703	0.95[JPT][hapmap]
rs13114104	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13133016	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138648	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13147824	0.95[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1356787	0.91[JPT][hapmap]
rs1356788	0.85[EUR][1000 genomes]
rs1401912	0.95[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1464286	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1474178	0.81[EUR][1000 genomes]
rs1976815	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1996650	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2030362	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030365	0.92[EUR][1000 genomes]
rs2139512	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292985	0.83[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2899063	0.95[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs3796542	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3796547	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs3822003	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4167	0.95[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4864578	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4864581	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865087	0.86[EUR][1000 genomes]
rs4865090	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865100	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4865101	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6554348	0.81[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554349	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554352	0.92[EUR][1000 genomes]
rs6554355	0.95[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6554356	0.95[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6584	0.91[JPT][hapmap]
rs6812041	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6816268	0.91[JPT][hapmap]
rs6826795	0.91[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6830518	0.91[JPT][hapmap]
rs6834736	0.81[YRI][hapmap]
rs6836864	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841016	0.81[EUR][1000 genomes]
rs6848187	0.91[JPT][hapmap]
rs6856845	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657711	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7661712	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7683781	0.95[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7689163	0.87[JPT][hapmap]
rs7692385	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693137	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693683	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9312673	0.83[ASN][1000 genomes]
rs9683679	0.95[CEU][hapmap];0.80[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9684298	0.95[CEU][hapmap];0.80[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9997639	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13141793	AASDH	cis	parietal	SCAN
rs13141793	PPAT	cis	lymphoblastoid	seeQTL
rs13141793	AASDH	cis	cerebellum	SCAN
rs13141793	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13141793	USP46	cis	cerebellum	SCAN
rs13141793	AASDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
3	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
4	chr4:57203200-57251800	Weak transcription	A549	lung
5	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:57204000-57252200	Weak transcription	NH-A	brain
7	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
9	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
12	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:57213400-57252200	Weak transcription	NHLF	lung
15	chr4:57213600-57250200	Weak transcription	K562	blood
16	chr4:57213600-57252000	Weak transcription	HMEC	breast
17	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:57216000-57251800	Weak transcription	HepG2	liver
21	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
24	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
25	chr4:57223200-57253200	Weak transcription	Gastric	stomach
26	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
27	chr4:57225000-57252200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:57227400-57252400	Weak transcription	NHEK	skin
29	chr4:57229800-57248200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:57229800-57251800	Weak transcription	Thymus	Thymus
31	chr4:57229800-57252400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:57229800-57252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:57229800-57252400	Weak transcription	Brain Germinal Matrix	brain
34	chr4:57229800-57253000	Weak transcription	Ovary	ovary
35	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:57232800-57252400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:57232800-57252400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:57232800-57253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:57235600-57252400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:57236400-57251800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:57236400-57252200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:57236600-57248200	Weak transcription	Fetal Lung	lung
44	chr4:57236600-57252400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:57236600-57253000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:57236600-57253200	Weak transcription	Lung	lung
47	chr4:57236800-57253000	Weak transcription	Aorta	Aorta
48	chr4:57236800-57253000	Weak transcription	Left Ventricle	heart
49	chr4:57237000-57252400	Weak transcription	Osteobl	bone
50	chr4:57237000-57252600	Weak transcription	Fetal Stomach	stomach

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