Variant report

Variant	rs12129776
Chromosome Location	chr1:150231989-150231990
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:150231959-150232936	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:150231408-150233074	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr1:150231620-150232884	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFIC	chr1:150231885-150232912	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:150231963-150233108	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150212531..150214773-chr1:150230839..150232375,2	MCF-7	breast:
2	chr1:150207177..150209173-chr1:150229648..150233094,4	MCF-7	breast:
3	chr1:150230739..150232605-chr1:150292549..150295461,2	MCF-7	breast:
4	chr1:150230902..150233122-chr1:150898050..150900989,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271845	TF binding region
CA14	TF binding region
ENSG00000238526	TF binding region
ENSG00000143379	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10494266	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2275780	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12129776	TARS2	cis	frontal cortex	BrainEAC

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150227800-150233200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:150228000-150232000	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:150228000-150232400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:150228000-150232600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:150228200-150233000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:150228200-150233200	Enhancers	Fetal Lung	lung
7	chr1:150228400-150232400	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr1:150228600-150232200	Enhancers	K562	blood
9	chr1:150228600-150232800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:150228800-150232400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr1:150229200-150232400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:150229200-150232800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:150229200-150232800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:150229600-150232200	Weak transcription	Pancreas	Pancrea
15	chr1:150229600-150232400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:150229600-150233000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:150229600-150236000	Weak transcription	Lung	lung
18	chr1:150229800-150232400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr1:150229800-150233000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:150230000-150233000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:150230200-150232800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr1:150230200-150233600	Weak transcription	Spleen	Spleen
23	chr1:150230400-150232000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:150230400-150232000	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr1:150230400-150233000	Enhancers	Ovary	ovary
26	chr1:150230800-150232000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:150230800-150232000	Flanking Active TSS	HepG2	liver
28	chr1:150230800-150233000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:150230800-150233000	Enhancers	Fetal Stomach	stomach
30	chr1:150230800-150236000	Weak transcription	Right Ventricle	heart
31	chr1:150230800-150239400	Weak transcription	Fetal Brain Male	brain
32	chr1:150230800-150239400	Weak transcription	Right Atrium	heart
33	chr1:150231000-150232200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:150231000-150232200	Enhancers	Fetal Muscle Leg	muscle
35	chr1:150231000-150232200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:150231000-150232400	Enhancers	Colon Smooth Muscle	Colon
37	chr1:150231000-150232600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:150231200-150232000	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr1:150231200-150232000	Enhancers	Hela-S3	cervix
40	chr1:150231200-150232200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:150231200-150232200	Enhancers	Stomach Mucosa	stomach
42	chr1:150231200-150233000	Flanking Active TSS	Fetal Heart	heart
43	chr1:150231200-150233000	Enhancers	Psoas Muscle	Psoas
44	chr1:150231200-150235600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:150231400-150232000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr1:150231400-150232200	Weak transcription	Left Ventricle	heart
47	chr1:150231400-150232600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:150231600-150232000	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr1:150231600-150232000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:150231600-150232200	Enhancers	Colonic Mucosa	Colon

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