Variant report

Variant	rs590329
Chromosome Location	chr6:144607307-144607308
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	chr6:133135604..133137467-chr6:144606007..144608305,2	K562	blood:
2	chr6:144606824..144608686-chr6:144612293..144613805,2	K562	blood:

Variant related genes	Relation type
ENSG00000206754	Chromatin interaction
ENSG00000152818	Chromatin interaction
ENSG00000112306	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs583341	0.85[ASN][1000 genomes]
rs584283	0.85[ASN][1000 genomes]
rs586016	0.85[ASN][1000 genomes]
rs586471	0.85[ASN][1000 genomes]
rs586553	0.83[ASN][1000 genomes]
rs587691	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs589892	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs590362	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591311	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs592388	0.85[ASN][1000 genomes]
rs592667	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs598222	0.85[ASN][1000 genomes]
rs599074	0.85[ASN][1000 genomes]
rs601816	0.83[AFR][1000 genomes]
rs601873	0.83[AFR][1000 genomes]
rs602764	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs603692	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs612928	0.86[ASN][1000 genomes]
rs615755	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs616619	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs619750	0.85[ASN][1000 genomes]
rs623320	0.85[ASN][1000 genomes]
rs632972	0.84[ASN][1000 genomes]
rs633106	0.81[AFR][1000 genomes]
rs633802	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs643596	0.80[ASN][1000 genomes]
rs644124	0.81[ASN][1000 genomes]
rs649426	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs652262	0.85[ASN][1000 genomes]
rs659899	0.84[ASN][1000 genomes]
rs660286	0.85[ASN][1000 genomes]
rs660307	0.85[ASN][1000 genomes]
rs660770	0.85[ASN][1000 genomes]
rs662419	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs664541	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs664721	0.85[ASN][1000 genomes]
rs665135	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs667740	0.85[ASN][1000 genomes]
rs667765	0.85[ASN][1000 genomes]
rs672468	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs676859	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs680093	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs681854	0.85[ASN][1000 genomes]
rs681916	0.85[ASN][1000 genomes]
rs682704	0.85[ASN][1000 genomes]
rs849661	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[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	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590329	RP1-83M4.2	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144604800-144608400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:144604800-144608800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:144604800-144608800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:144604800-144608800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:144604800-144609000	Active TSS	Brain Anterior Caudate	brain
6	chr6:144605000-144607400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:144605000-144607800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:144605000-144608600	Active TSS	Brain Hippocampus Middle	brain
9	chr6:144605000-144608800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:144605000-144608800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:144605000-144608800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:144605000-144608800	Active TSS	Fetal Lung	lung
13	chr6:144605000-144608800	Active TSS	Right Atrium	heart
14	chr6:144605000-144608800	Active TSS	Right Ventricle	heart
15	chr6:144605000-144608800	Active TSS	NHLF	lung
16	chr6:144605000-144609000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:144605000-144609000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:144605000-144609000	Active TSS	Ovary	ovary
19	chr6:144605000-144609000	Active TSS	Psoas Muscle	Psoas
20	chr6:144605000-144609600	Active TSS	Stomach Smooth Muscle	stomach
21	chr6:144605200-144607800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:144605200-144608200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:144605200-144608400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:144605200-144608600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr6:144605200-144608600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:144605200-144608600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:144605200-144608600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:144605200-144608600	Active TSS	Colonic Mucosa	Colon
29	chr6:144605200-144608600	Active TSS	Fetal Heart	heart
30	chr6:144605200-144608600	Active TSS	Fetal Muscle Trunk	muscle
31	chr6:144605200-144608800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:144605200-144608800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:144605200-144608800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:144605200-144608800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:144605200-144608800	Active TSS	Fetal Kidney	kidney
36	chr6:144605200-144608800	Active TSS	Rectal Smooth Muscle	rectum
37	chr6:144605200-144609000	Active TSS	Aorta	Aorta
38	chr6:144605200-144609000	Active TSS	Brain Angular Gyrus	brain
39	chr6:144605200-144609000	Active TSS	Left Ventricle	heart
40	chr6:144605200-144609000	Active TSS	A549	lung
41	chr6:144605200-144609000	Active TSS	NHDF-Ad	bronchial
42	chr6:144605400-144607400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:144605400-144608600	Active TSS	Lung	lung
44	chr6:144605400-144608600	Active TSS	Pancreas	Pancrea
45	chr6:144605400-144608600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr6:144605400-144608600	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:144605400-144608600	Active TSS	Stomach Mucosa	stomach
48	chr6:144605400-144608800	Active TSS	Fetal Intestine Large	intestine
49	chr6:144605400-144608800	Active TSS	Fetal Intestine Small	intestine
50	chr6:144605400-144608800	Active TSS	Fetal Muscle Leg	muscle

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