Variant report

Variant	rs57417995
Chromosome Location	chr1:172108145-172108146
allele	A/G
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	chr1:172105998-172108187	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:172106068-172111567	PFSK-1	brain:	n/a	n/a
3	USF1	chr1:172107741-172108172	ECC-1	luminal epithelium:	n/a	n/a
4	USF1	chr1:172107722-172108192	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:172107763-172108164	PFSK-1	brain:	n/a	n/a
6	USF1	chr1:172107819-172108188	ECC-1	luminal epithelium:	n/a	n/a
7	STAT3	chr1:172107987-172108196	MCF10A-Er-Src	breast:	n/a	chr1:172108128-172108140
8	USF1	chr1:172107801-172108161	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-1	chr1:172106019-172113975	NONHSAT007596
2	lnc-PIGC-1	chr1:172106019-172109736	NONHSAT007597
3	lnc-PIGC-1	chr1:172107724-172113975	NONHSAT007598

Variant related genes	Relation type
MIR214	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10489299	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12564349	0.88[ASN][1000 genomes]
rs12569096	0.88[ASN][1000 genomes]
rs16843915	0.99[ASN][1000 genomes]
rs16843935	0.88[ASN][1000 genomes]
rs59665490	0.97[ASN][1000 genomes]
rs60077625	0.81[ASN][1000 genomes]
rs60255562	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172062400-172109200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:172077200-172110600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
5	chr1:172090000-172109600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:172090400-172108800	Weak transcription	Fetal Stomach	stomach
7	chr1:172094600-172110600	Weak transcription	Left Ventricle	heart
8	chr1:172096400-172110600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:172100200-172108600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:172102000-172113400	Weak transcription	Lung	lung
11	chr1:172102600-172113400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:172102600-172113600	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:172103200-172110400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:172103800-172109200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:172105400-172109600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:172106200-172109400	Weak transcription	NH-A	brain
17	chr1:172106400-172109000	Weak transcription	HUVEC	blood vessel
18	chr1:172107000-172108600	Weak transcription	Fetal Kidney	kidney
19	chr1:172107200-172108600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:172107200-172109800	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:172107400-172108400	Genic enhancers	Fetal Lung	lung
22	chr1:172107400-172109000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:172107600-172108200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:172107600-172108200	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr1:172107600-172108400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:172107600-172108400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:172107600-172108800	Enhancers	HMEC	breast
28	chr1:172107600-172108800	Enhancers	NHEK	skin
29	chr1:172107800-172108200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:172107800-172108200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:172107800-172108200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:172107800-172108200	Enhancers	Psoas Muscle	Psoas
33	chr1:172107800-172108200	Flanking Active TSS	Right Atrium	heart
34	chr1:172107800-172108400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:172107800-172108600	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr1:172107800-172108600	Strong transcription	HSMM	muscle
37	chr1:172107800-172108800	Genic enhancers	NHLF	lung
38	chr1:172107800-172109000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:172107800-172109200	Genic enhancers	Osteobl	bone
40	chr1:172107800-172109400	Weak transcription	Fetal Intestine Large	intestine
41	chr1:172107800-172110400	Weak transcription	Fetal Intestine Small	intestine
42	chr1:172107800-172111400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
43	chr1:172108000-172108200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:172108000-172108200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:172108000-172108200	Weak transcription	Esophagus	oesophagus
46	chr1:172108000-172108200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
47	chr1:172108000-172108600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:172108000-172108600	Active TSS	Adipose Nuclei	Adipose
49	chr1:172108000-172108800	Active TSS	Aorta	Aorta
50	chr1:172108000-172112400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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