Variant report

Variant	rs13150967
Chromosome Location	chr4:57246019-57246020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 67 )
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];0.93[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124570	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722404	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11723379	0.81[EUR][1000 genomes]
rs11728068	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734595	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935357	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11937997	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11943048	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946745	0.81[AMR][1000 genomes];0.89[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114481	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13122422	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123542	0.80[AMR][1000 genomes];0.97[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13131846	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13132553	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13134963	0.85[CEU][hapmap]
rs13135151	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13140746	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13148435	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13148656	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]
rs13150137	0.91[ASN][1000 genomes]
rs1401908	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030363	0.85[EUR][1000 genomes]
rs2176785	0.85[CEU][hapmap]
rs3796544	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];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554346	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6554353	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554354	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811153	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[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];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6811652	0.85[EUR][1000 genomes]
rs6812222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6815480	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6818283	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6818340	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6820922	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6823339	0.83[EUR][1000 genomes]
rs6854326	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6857561	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7437329	0.92[CEU][hapmap];0.85[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];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7656361	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7673373	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682041	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7682608	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7695701	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7699157	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs956275	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995463	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13150967	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs13150967	AASDH	cis	cerebellum	SCAN
rs13150967	AASDH	cis	parietal	SCAN
rs13150967	RPL21P44	cis	cerebellum	SCAN
rs13150967	AASDH	cis	multi-tissue	Pritchard
rs13150967	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13150967	AASDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 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	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
25	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
26	chr4:57223200-57253200	Weak transcription	Gastric	stomach
27	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
28	chr4:57225000-57252200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:57227400-57252400	Weak transcription	NHEK	skin
30	chr4:57229800-57248200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:57229800-57251800	Weak transcription	Thymus	Thymus
32	chr4:57229800-57252400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:57229800-57252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:57229800-57252400	Weak transcription	Brain Germinal Matrix	brain
35	chr4:57229800-57253000	Weak transcription	Ovary	ovary
36	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:57232800-57246800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:57232800-57252400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:57232800-57252400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:57232800-57253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:57235600-57252400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:57236400-57246800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:57236400-57251800	Weak transcription	Brain Angular Gyrus	brain
45	chr4:57236400-57252200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:57236600-57248200	Weak transcription	Fetal Lung	lung
47	chr4:57236600-57252400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:57236600-57253000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:57236600-57253200	Weak transcription	Lung	lung
50	chr4:57236800-57246200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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