Variant report

Variant	rs11722404
Chromosome Location	chr4:57238064-57238065
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	chr4:57237069..57240019-chr4:57249640..57251353,2	K562	blood:
2	chr4:57237841..57240347-chr4:57243784..57245813,2	K562	blood:

Variant related genes	Relation type
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1042040	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124570	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11538098	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11723379	0.81[EUR][1000 genomes]
rs11728068	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11732985	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11734595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11935357	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11937997	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11943048	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11946745	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13109030	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13114481	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13122196	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13122422	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13122832	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13123542	0.91[ASN][1000 genomes]
rs13124065	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13129188	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13135151	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13146014	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13148435	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13148656	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150137	0.86[ASN][1000 genomes]
rs13150967	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1401908	0.85[EUR][1000 genomes]
rs1401911	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2030363	0.85[EUR][1000 genomes]
rs3796544	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554346	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554350	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811153	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811616	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811652	0.85[EUR][1000 genomes]
rs6812222	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815480	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818283	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6818340	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6820922	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6823339	0.83[EUR][1000 genomes]
rs6854326	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6857561	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7437329	0.85[EUR][1000 genomes]
rs7654543	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682041	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682608	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7695701	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7699157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956275	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995463	0.96[EUR][1000 genomes];0.81[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11722404	AASDH	cis	multi-tissue	Pritchard
rs11722404	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs11722404	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs11722404	AASDH	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:114 , 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	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
4	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
5	chr4:57203200-57251800	Weak transcription	A549	lung
6	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:57204000-57252200	Weak transcription	NH-A	brain
8	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
10	chr4:57207800-57253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:57211000-57251600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr4:57211800-57252200	Weak transcription	Fetal Heart	heart
13	chr4:57212400-57251800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:57213000-57244200	Weak transcription	Spleen	Spleen
15	chr4:57213400-57251600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:57213400-57252200	Weak transcription	NHLF	lung
17	chr4:57213600-57250200	Weak transcription	K562	blood
18	chr4:57213600-57252000	Weak transcription	HMEC	breast
19	chr4:57214400-57251800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:57214600-57252200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:57215800-57251600	Weak transcription	Brain Anterior Caudate	brain
22	chr4:57216000-57241200	Weak transcription	Pancreas	Pancrea
23	chr4:57216000-57251800	Weak transcription	HepG2	liver
24	chr4:57216000-57252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:57216000-57253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:57216200-57245600	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:57216200-57246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:57216200-57246200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:57216400-57251800	Weak transcription	Psoas Muscle	Psoas
30	chr4:57218400-57239000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:57218400-57241200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:57220600-57243400	Weak transcription	HSMM	muscle
33	chr4:57223000-57253200	Weak transcription	Esophagus	oesophagus
34	chr4:57223200-57253200	Weak transcription	Gastric	stomach
35	chr4:57223600-57251600	Weak transcription	Fetal Kidney	kidney
36	chr4:57225000-57243600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:57225000-57252200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:57226600-57245800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:57227400-57252400	Weak transcription	NHEK	skin
40	chr4:57229800-57244000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:57229800-57248200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:57229800-57251800	Weak transcription	Thymus	Thymus
43	chr4:57229800-57252400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:57229800-57252400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:57229800-57252400	Weak transcription	Brain Germinal Matrix	brain
46	chr4:57229800-57253000	Weak transcription	Ovary	ovary
47	chr4:57229800-57253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:57229800-57253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:57232800-57246800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr4:57232800-57252400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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