Variant report

Variant	rs12047492
Chromosome Location	chr1:172110765-172110766
allele	A/G
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:2)
LncRNA
region (count:2)
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	GATA3	chr1:172110724-172110879	SH-SY5Y	brain:	n/a	n/a
2	GATA2	chr1:172110491-172111158	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:172106068-172111567	PFSK-1	brain:	n/a	n/a
4	SIN3AK20	chr1:172110741-172110995	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:172110385-172111427	SK-N-SH	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172109737..172112011-chr1:172117848..172120682,2	K562	blood:
2	chr1:172106852..172108519-chr1:172110470..172112624,2	K562	blood:

(count:2 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10218612	0.93[JPT][hapmap]
rs10442603	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10489730	0.88[JPT][hapmap]
rs10797719	0.88[JPT][hapmap]
rs10797735	0.89[JPT][hapmap]
rs10797791	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10910966	0.88[JPT][hapmap]
rs10911101	1.00[CEU][hapmap];0.84[JPT][hapmap];0.98[EUR][1000 genomes]
rs10911109	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10911110	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10911111	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs10911112	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911116	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10911121	0.94[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs10911122	0.87[AMR][1000 genomes]
rs10911123	0.87[AMR][1000 genomes]
rs10911124	0.94[CEU][hapmap]
rs10911125	0.94[CEU][hapmap]
rs12120556	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12141278	0.97[EUR][1000 genomes]
rs1475230	0.94[CEU][hapmap]
rs1475231	0.94[CEU][hapmap]
rs1555383	0.88[JPT][hapmap]
rs2038481	0.88[JPT][hapmap]
rs2057302	0.88[JPT][hapmap]
rs2146901	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2181624	1.00[CEU][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2208367	0.89[JPT][hapmap]
rs2295610	0.88[JPT][hapmap]
rs2295611	0.88[JPT][hapmap]
rs2421985	0.89[ASN][1000 genomes]
rs2421986	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421987	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs3736791	0.88[JPT][hapmap]
rs4076678	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs4604727	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs6425599	0.88[JPT][hapmap]
rs6669406	0.89[JPT][hapmap]
rs72719075	0.88[EUR][1000 genomes]
rs733189	0.89[ASN][1000 genomes]
rs733190	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs733191	0.95[CHB][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs7518865	0.88[JPT][hapmap]
rs7530970	0.88[JPT][hapmap]
rs9286842	0.88[JPT][hapmap]

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:69 , 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	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
3	chr1:172102000-172113400	Weak transcription	Lung	lung
4	chr1:172102600-172113400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:172102600-172113600	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:172107800-172111400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
7	chr1:172108000-172112400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:172108000-172112600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:172108000-172115000	Active TSS	Ovary	ovary
10	chr1:172108200-172112400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:172108200-172113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:172108200-172115000	Active TSS	Right Atrium	heart
13	chr1:172108400-172111800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:172108400-172112800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:172108600-172110800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:172108600-172111000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
17	chr1:172108600-172114400	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:172108800-172110800	Active TSS	Adipose Nuclei	Adipose
19	chr1:172108800-172112400	Weak transcription	NHEK	skin
20	chr1:172108800-172112600	Weak transcription	HMEC	breast
21	chr1:172108800-172114400	Active TSS	Fetal Stomach	stomach
22	chr1:172109000-172112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:172109000-172114400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:172109200-172111600	Transcr. at gene 5' and 3'	Osteobl	bone
25	chr1:172109400-172114400	Active TSS	Fetal Intestine Large	intestine
26	chr1:172109600-172111800	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:172109600-172114600	Active TSS	NHLF	lung
28	chr1:172109800-172111800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:172109800-172114800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:172109800-172115200	Active TSS	Colon Smooth Muscle	Colon
31	chr1:172110000-172112600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:172110000-172114400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:172110000-172114600	Flanking Active TSS	HUVEC	blood vessel
34	chr1:172110200-172110800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:172110200-172111000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:172110200-172111000	Enhancers	Brain Germinal Matrix	brain
37	chr1:172110200-172111200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:172110200-172115000	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:172110200-172115000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:172110400-172110800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr1:172110400-172110800	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr1:172110400-172111000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr1:172110400-172111200	Flanking Active TSS	NH-A	brain
44	chr1:172110400-172113400	Active TSS	Psoas Muscle	Psoas
45	chr1:172110400-172114000	Active TSS	HSMMtube	muscle
46	chr1:172110400-172114200	Active TSS	HSMM	muscle
47	chr1:172110400-172114400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr1:172110400-172114600	Active TSS	Aorta	Aorta
49	chr1:172110400-172114600	Active TSS	Fetal Intestine Small	intestine
50	chr1:172110400-172114600	Active TSS	Placenta	Placenta

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