Variant report

Variant	rs2819530
Chromosome Location	chr1:172112954-172112955
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	GATA3	chr1:172112404-172113104	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr1:172112463-172113064	SK-N-SH_RA	brain:	n/a	n/a
3	MAFK	chr1:172112767-172113069	IMR90	lung:	n/a	chr1:172112928-172112937
4	EP300	chr1:172112331-172113060	SK-N-SH	brain:	n/a	chr1:172112506-172112520 chr1:172112730-172112739 chr1:172112419-172112429
5	NFIC	chr1:172112303-172113136	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr1:172112417-172114929	IMR90	lung:	n/a	n/a
7	TCF12	chr1:172112349-172113004	SK-N-SH	brain:	n/a	chr1:172112684-172112694
8	TAF1	chr1:172112488-172113131	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr1:172112432-172113189	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr1:172112387-172113003	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:172111853-172114971	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr1:172112664-172113166	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr1:172112864-172113031	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:172112892-172113092	MCF10A-Er-Src	breast:	n/a	chr1:172112928-172112940 chr1:172112929-172112939 chr1:172112929-172112939
15	FOS	chr1:172112832-172113079	MCF10A-Er-Src	breast:	n/a	chr1:172112928-172112940 chr1:172112929-172112939 chr1:172112929-172112939
16	TCF12	chr1:172112289-172113200	SK-N-SH	brain:	n/a	chr1:172112684-172112694
17	POLR2A	chr1:172111943-172113172	PFSK-1	brain:	n/a	n/a
18	TAF1	chr1:172112585-172113048	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr1:172112453-172113101	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr1:172112343-172113157	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	chr1:172107724-172113975	NONHSAT007598

Variant related genes	Relation type
MIR214	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10752864	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10911004	0.81[ASN][1000 genomes]
rs12029864	0.83[ASN][1000 genomes]
rs12075807	0.83[JPT][hapmap]
rs12091015	0.83[JPT][hapmap]
rs1555381	0.83[JPT][hapmap]
rs2421985	0.80[EUR][1000 genomes]
rs2761183	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2819527	0.83[JPT][hapmap]
rs35665317	0.81[ASN][1000 genomes]
rs4075021	0.91[CHD][hapmap];0.81[GIH][hapmap];0.93[ASN][1000 genomes]
rs4244192	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs495590	0.85[CHB][hapmap];0.97[CHD][hapmap];0.81[LWK][hapmap];0.82[TSI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6671218	0.93[ASN][1000 genomes]
rs6676154	0.93[ASN][1000 genomes]
rs6693520	0.97[ASN][1000 genomes]
rs733190	0.85[CEU][hapmap]
rs733191	0.85[CEU][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:79 , 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	chr1:172108000-172115000	Active TSS	Ovary	ovary
6	chr1:172108200-172113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:172108200-172115000	Active TSS	Right Atrium	heart
8	chr1:172108600-172114400	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:172108800-172114400	Active TSS	Fetal Stomach	stomach
10	chr1:172109000-172114400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:172109400-172114400	Active TSS	Fetal Intestine Large	intestine
12	chr1:172109600-172114600	Active TSS	NHLF	lung
13	chr1:172109800-172114800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:172109800-172115200	Active TSS	Colon Smooth Muscle	Colon
15	chr1:172110000-172114400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:172110000-172114600	Flanking Active TSS	HUVEC	blood vessel
17	chr1:172110200-172115000	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:172110200-172115000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:172110400-172113400	Active TSS	Psoas Muscle	Psoas
20	chr1:172110400-172114000	Active TSS	HSMMtube	muscle
21	chr1:172110400-172114200	Active TSS	HSMM	muscle
22	chr1:172110400-172114400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr1:172110400-172114600	Active TSS	Aorta	Aorta
24	chr1:172110400-172114600	Active TSS	Fetal Intestine Small	intestine
25	chr1:172110400-172114600	Active TSS	Placenta	Placenta
26	chr1:172110400-172114800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:172110400-172114800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:172110400-172114800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:172110600-172113200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:172110600-172114400	Active TSS	Right Ventricle	heart
31	chr1:172110600-172114600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:172110800-172114200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:172110800-172114800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:172111000-172113400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:172111000-172113600	Weak transcription	Brain Angular Gyrus	brain
36	chr1:172111200-172113400	Active TSS	Adipose Nuclei	Adipose
37	chr1:172111200-172114200	Active TSS	Fetal Lung	lung
38	chr1:172111200-172114400	Active TSS	Fetal Kidney	kidney
39	chr1:172111400-172114200	Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:172111400-172114400	Active TSS	NHDF-Ad	bronchial
41	chr1:172111600-172113400	Weak transcription	Colonic Mucosa	Colon
42	chr1:172111600-172114400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:172111600-172114400	Active TSS	Osteobl	bone
44	chr1:172111800-172113600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:172111800-172113800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:172111800-172114200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:172111800-172115000	Active TSS	Fetal Muscle Leg	muscle
48	chr1:172112400-172113000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:172112400-172113600	Enhancers	NHEK	skin
50	chr1:172112400-172113800	Active TSS	Small Intestine	intestine

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