Variant report

Variant	rs12071663
Chromosome Location	chr1:173815290-173815291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173808666..173811238-chr1:173814911..173817851,2	MCF-7	breast:
2	chr1:173814385..173815973-chr1:173816216..173818927,2	MCF-7	breast:
3	chr1:173812839..173816033-chr1:173816444..173819357,4	K562	blood:
4	chr1:173813848..173815354-chr1:173868655..173871235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10798295	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10912676	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12071594	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12078824	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1322770	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322775	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1322777	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1322780	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1799876	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065171	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4606360	0.81[ASN][1000 genomes]
rs4652229	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5877	0.93[EUR][1000 genomes]
rs5878	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6663875	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349095	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7544605	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7552939	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9286895	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs941989	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9425430	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425435	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425755	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425765	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9425766	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9661233	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12071663	DARS2	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173820600	Weak transcription	NHLF	lung
3	chr1:173794600-173821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:173794600-173821800	Weak transcription	Pancreas	Pancrea
5	chr1:173794600-173822000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
10	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
12	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:173795200-173822400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:173795200-173824600	Weak transcription	Gastric	stomach
15	chr1:173795400-173817400	Weak transcription	Fetal Brain Male	brain
16	chr1:173796000-173818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:173796200-173817800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:173797800-173815800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:173798400-173815600	Strong transcription	Dnd41	blood
21	chr1:173798800-173816000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:173799400-173815800	Strong transcription	Placenta	Placenta
23	chr1:173799400-173815800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:173799400-173820400	Strong transcription	Fetal Intestine Large	intestine
25	chr1:173799600-173817000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:173799800-173815600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:173799800-173816000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:173801000-173822200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:173801200-173825000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:173802000-173816000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:173802000-173816000	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:173802000-173816000	Strong transcription	Fetal Thymus	thymus
34	chr1:173802200-173817800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:173802600-173816000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:173804600-173819000	Weak transcription	GM12878-XiMat	blood
38	chr1:173804800-173816000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:173805200-173816400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:173805800-173816000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:173806400-173816600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:173806800-173815600	Strong transcription	Thymus	Thymus
43	chr1:173806800-173822800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:173809000-173822000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:173809200-173825200	Weak transcription	NHDF-Ad	bronchial
46	chr1:173809400-173816000	Strong transcription	Fetal Intestine Small	intestine
47	chr1:173809400-173816000	Strong transcription	Fetal Stomach	stomach
48	chr1:173809800-173815400	Weak transcription	HepG2	liver
49	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
50	chr1:173810200-173822000	Weak transcription	Fetal Kidney	kidney

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