Variant report

Variant	rs6588647
Chromosome Location	chr1:57160869-57160870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10749709	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10889002	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10889003	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11206891	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12134054	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12138351	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12402675	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12405291	0.90[EUR][1000 genomes]
rs12759063	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2051040	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2143749	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2746342	0.85[AMR][1000 genomes]
rs2796542	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4451572	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4561065	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4912408	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4912411	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6588645	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6588646	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6663750	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676950	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6688242	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6688263	0.87[AMR][1000 genomes];0.92[EUR][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	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv1831276	chr1:57139370-57175158	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57122800-57169600	Weak transcription	Ovary	ovary
2	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
3	chr1:57136200-57161400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
7	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:57149600-57166000	Weak transcription	Right Ventricle	heart
9	chr1:57150000-57165800	Weak transcription	Left Ventricle	heart
10	chr1:57150600-57168000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:57151000-57165600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:57151400-57165400	Weak transcription	Fetal Heart	heart
13	chr1:57152400-57165800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:57154200-57174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:57154400-57166000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:57154400-57169000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:57154400-57174600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:57154400-57174800	Weak transcription	Gastric	stomach
19	chr1:57154600-57165200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:57154600-57169800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:57154800-57161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:57154800-57162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:57154800-57165800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:57154800-57166000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:57155000-57161400	Weak transcription	HepG2	liver
26	chr1:57155000-57162200	Weak transcription	A549	lung
27	chr1:57156600-57165800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:57158400-57169000	Weak transcription	Hela-S3	cervix
29	chr1:57158800-57161400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:57158800-57166000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:57159000-57166000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:57159200-57166600	Weak transcription	Brain Germinal Matrix	brain
33	chr1:57159600-57172800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:57159800-57174800	Weak transcription	Fetal Stomach	stomach
35	chr1:57160000-57162000	Weak transcription	Fetal Brain Female	brain
36	chr1:57160000-57174800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:57160200-57162400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:57160200-57174600	Weak transcription	Fetal Brain Male	brain
39	chr1:57160400-57165400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:57160400-57166000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:57160400-57174800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:57160600-57161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:57160800-57165600	Weak transcription	Rectal Mucosa Donor 29	rectum

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