Variant report

Variant	rs6826909
Chromosome Location	chr4:47909435-47909436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47892858..47895013-chr4:47908321..47910117,3	K562	blood:
2	chr4:47908070..47910141-chr4:47912067..47913855,3	MCF-7	breast:
3	chr4:47901821..47910002-chr4:47912490..47917520,12	MCF-7	breast:
4	chr4:47907905..47911619-chr4:47914071..47917997,8	K562	blood:
5	chr4:47892858..47894534-chr4:47908368..47910117,2	K562	blood:
6	chr4:47905358..47911126-chr4:47914297..47917984,8	MCF-7	breast:
7	chr4:47906567..47911619-chr4:47914438..47917527,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPAL1-3	chr4:47909419-47909539	NONHSAT096264

No data

Variant related genes	Relation type
ENSG00000163293	Chromatin interaction
ENSG00000170448	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10002498	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036681	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10938498	0.82[EUR][1000 genomes]
rs10938508	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11732840	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1371728	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1440222	1.00[ASN][1000 genomes]
rs1545200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550444	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808853	0.87[EUR][1000 genomes]
rs1812964	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	1.00[ASN][1000 genomes]
rs1968542	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2033895	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.85[EUR][1000 genomes]
rs2119207	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.87[ASN][1000 genomes]
rs2352456	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.89[ASN][1000 genomes]
rs321640	1.00[ASN][1000 genomes]
rs321641	0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.87[ASN][1000 genomes]
rs3762858	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762859	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4555602	0.82[AFR][1000 genomes]
rs4694868	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694875	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4694878	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.89[EUR][1000 genomes]
rs4695296	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4695302	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695309	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6447596	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.84[EUR][1000 genomes]
rs6815975	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6819506	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833320	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845451	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850142	0.80[EUR][1000 genomes]
rs707723	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672090	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893861	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291318	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6826909	CNGA1	cis	Heart Left Ventricle	GTEx
rs6826909	CNGA1	cis	Muscle Skeletal	GTEx
rs6826909	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47865400-47913400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:47872400-47911600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:47873400-47913400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:47873600-47910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:47874400-47913400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:47874400-47913600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
9	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:47877400-47913800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:47877600-47913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:47877800-47910200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
15	chr4:47882800-47913000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:47883200-47913600	Strong transcription	HMEC	breast
17	chr4:47883200-47913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:47883200-47914400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:47884200-47913000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:47889800-47913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:47890400-47913800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:47890400-47914200	Strong transcription	Liver	Liver
23	chr4:47890600-47910200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:47890800-47909600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:47890800-47913000	Strong transcription	Placenta	Placenta
26	chr4:47894600-47915200	Weak transcription	Aorta	Aorta
27	chr4:47894600-47915200	Weak transcription	Gastric	stomach
28	chr4:47895000-47913800	Weak transcription	Fetal Heart	heart
29	chr4:47896400-47912600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:47897800-47909800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr4:47898200-47915200	Weak transcription	Small Intestine	intestine
32	chr4:47898400-47915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:47898400-47915200	Weak transcription	Colonic Mucosa	Colon
34	chr4:47898600-47915200	Weak transcription	Fetal Brain Male	brain
35	chr4:47899600-47915600	Weak transcription	Lung	lung
36	chr4:47899800-47915000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr4:47899800-47915200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:47899800-47915200	Weak transcription	Brain Substantia Nigra	brain
39	chr4:47900000-47912000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:47900000-47913800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:47900000-47914000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:47900000-47915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:47900200-47915200	Weak transcription	HSMMtube	muscle
44	chr4:47900600-47915200	Weak transcription	Thymus	Thymus
45	chr4:47901000-47913600	Weak transcription	NHLF	lung
46	chr4:47901000-47915200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:47901000-47915200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr4:47901000-47915200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:47901200-47915000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:47901200-47915200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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