Variant report

Variant	rs59665490
Chromosome Location	chr1:172112151-172112152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:172111853-172114971	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:172111943-172113172	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172106852..172108519-chr1:172110470..172112624,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-1	chr1:172106019-172113975	NONHSAT007596
2	lnc-PIGC-1	chr1:172107724-172113975	NONHSAT007598

Variant related genes	Relation type
MIR214	TF binding region
ENSG00000207949	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10489299	0.96[ASN][1000 genomes]
rs12562173	1.00[EUR][1000 genomes]
rs12562275	1.00[EUR][1000 genomes]
rs12562403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12564349	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12568723	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12568908	1.00[EUR][1000 genomes]
rs12569096	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12569236	1.00[EUR][1000 genomes]
rs12569310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843801	1.00[EUR][1000 genomes]
rs16843816	1.00[EUR][1000 genomes]
rs16843819	1.00[EUR][1000 genomes]
rs16843820	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843827	1.00[EUR][1000 genomes]
rs16843831	1.00[EUR][1000 genomes]
rs16843837	1.00[EUR][1000 genomes]
rs16843841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843842	1.00[EUR][1000 genomes]
rs16843915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16843935	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3924561	1.00[EUR][1000 genomes]
rs57417995	0.97[ASN][1000 genomes]
rs60255562	0.92[ASN][1000 genomes]
rs73039343	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
2	chr1:172102000-172113400	Weak transcription	Lung	lung
3	chr1:172102600-172113400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:172102600-172113600	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:172108000-172112400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:172108000-172112600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:172108000-172115000	Active TSS	Ovary	ovary
8	chr1:172108200-172112400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:172108200-172113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:172108200-172115000	Active TSS	Right Atrium	heart
11	chr1:172108400-172112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:172108600-172114400	Active TSS	Stomach Smooth Muscle	stomach
13	chr1:172108800-172112400	Weak transcription	NHEK	skin
14	chr1:172108800-172112600	Weak transcription	HMEC	breast
15	chr1:172108800-172114400	Active TSS	Fetal Stomach	stomach
16	chr1:172109000-172112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:172109000-172114400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:172109400-172114400	Active TSS	Fetal Intestine Large	intestine
19	chr1:172109600-172114600	Active TSS	NHLF	lung
20	chr1:172109800-172114800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:172109800-172115200	Active TSS	Colon Smooth Muscle	Colon
22	chr1:172110000-172112600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:172110000-172114400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:172110000-172114600	Flanking Active TSS	HUVEC	blood vessel
25	chr1:172110200-172115000	Active TSS	Fetal Muscle Trunk	muscle
26	chr1:172110200-172115000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:172110400-172113400	Active TSS	Psoas Muscle	Psoas
28	chr1:172110400-172114000	Active TSS	HSMMtube	muscle
29	chr1:172110400-172114200	Active TSS	HSMM	muscle
30	chr1:172110400-172114400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr1:172110400-172114600	Active TSS	Aorta	Aorta
32	chr1:172110400-172114600	Active TSS	Fetal Intestine Small	intestine
33	chr1:172110400-172114600	Active TSS	Placenta	Placenta
34	chr1:172110400-172114800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:172110400-172114800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:172110400-172114800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:172110600-172112400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:172110600-172113200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:172110600-172114400	Active TSS	Right Ventricle	heart
40	chr1:172110600-172114600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:172110800-172112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:172110800-172114200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:172110800-172114800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:172111000-172112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:172111000-172112600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:172111000-172112600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:172111000-172112600	Weak transcription	Left Ventricle	heart
48	chr1:172111000-172112600	Weak transcription	Stomach Mucosa	stomach
49	chr1:172111000-172113400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:172111000-172113600	Weak transcription	Brain Angular Gyrus	brain

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