Variant report

Variant	rs12406184
Chromosome Location	chr1:57568608-57568609
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12405609	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12408256	0.87[EUR][1000 genomes]
rs12564278	0.87[EUR][1000 genomes]
rs12564961	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566320	0.87[EUR][1000 genomes]
rs17114978	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17115023	0.80[ASN][1000 genomes]
rs17115030	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17115105	0.87[EUR][1000 genomes]
rs17115108	0.87[EUR][1000 genomes]
rs17115146	0.87[EUR][1000 genomes]
rs17115155	0.87[EUR][1000 genomes]
rs17115222	0.86[EUR][1000 genomes]
rs17419873	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17420013	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17420181	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17420216	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17453874	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35522019	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs41286852	1.00[AFR][1000 genomes]
rs41286864	0.86[EUR][1000 genomes]
rs55706301	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61765266	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61765267	0.86[EUR][1000 genomes]
rs61765271	0.86[EUR][1000 genomes]
rs61765294	0.80[ASN][1000 genomes]
rs61765295	0.80[ASN][1000 genomes]
rs61765319	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61765320	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61765323	0.87[EUR][1000 genomes]
rs61765324	0.87[EUR][1000 genomes]
rs61765326	0.87[EUR][1000 genomes]
rs61765327	0.87[EUR][1000 genomes]
rs61765328	0.87[EUR][1000 genomes]
rs61765330	0.86[EUR][1000 genomes]
rs61765331	0.86[EUR][1000 genomes]
rs61765332	0.86[EUR][1000 genomes]
rs6697173	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs728719	0.80[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12406184	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57556800-57568800	Weak transcription	Right Atrium	heart
3	chr1:57565600-57569000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57566600-57568800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:57566600-57569400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:57566600-57569400	Enhancers	Fetal Lung	lung
7	chr1:57566800-57569400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:57567000-57570800	Enhancers	Fetal Heart	heart
9	chr1:57567400-57576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:57567600-57568800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:57567600-57569000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:57567600-57570800	Weak transcription	Brain Germinal Matrix	brain
13	chr1:57567800-57568800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:57568000-57568800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:57568000-57569800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:57568200-57569200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:57568400-57569000	Enhancers	Fetal Stomach	stomach
18	chr1:57568400-57569200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr1:57568400-57569200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:57568400-57569200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:57568400-57569200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:57568400-57569200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:57568400-57569800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:57568400-57571200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:57568600-57569200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:57568600-57569200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr1:57568600-57569200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:57568600-57569400	Enhancers	Fetal Muscle Leg	muscle
29	chr1:57568600-57569400	Enhancers	Left Ventricle	heart
30	chr1:57568600-57569400	Enhancers	Ovary	ovary

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