Variant report

Variant	rs6672018
Chromosome Location	chr1:114331315-114331316
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114295717..114297423-chr1:114329273..114331553,2	MCF-7	breast:
2	chr1:114328514..114333064-chr1:114341407..114344891,4	MCF-7	breast:
3	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
4	chr1:114330964..114333642-chr1:114352600..114356099,4	MCF-7	breast:
5	chr1:114330207..114332074-chr20:52046883..52049552,2	MCF-7	breast:
6	chr1:114328870..114331856-chr1:114340640..114342248,2	K562	blood:
7	chr1:114317996..114324872-chr1:114329159..114335059,8	K562	blood:
8	chr1:114324961..114329121-chr1:114330799..114335017,4	K562	blood:
9	chr1:114329880..114331707-chr1:114332071..114335621,3	K562	blood:
10	chr1:114300369..114304459-chr1:114329626..114333036,4	MCF-7	breast:
11	chr1:114330552..114332424-chr1:114422086..114424136,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1111695	0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs1217378	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1217379	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1217385	0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1217404	0.90[EUR][1000 genomes]
rs1217405	0.96[EUR][1000 genomes]
rs1217406	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1217409	0.94[EUR][1000 genomes]
rs1217411	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1217418	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1217419	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs1217420	0.95[EUR][1000 genomes]
rs1230682	0.81[ASN][1000 genomes]
rs1230686	0.81[ASN][1000 genomes]
rs1235005	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1310182	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1539437	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2185971	0.83[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs2273758	0.83[ASW][hapmap];0.81[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs2476600	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2476604	0.95[EUR][1000 genomes]
rs2797414	0.82[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs2797416	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3789598	0.82[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3789600	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4991898	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6537798	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6665194	0.82[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7555634	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6672018	MAGI3	cis	cerebellum	SCAN
rs6672018	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
5	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
6	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:114320000-114336200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:114320000-114340000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:114320200-114337200	Weak transcription	Placenta	Placenta
11	chr1:114320400-114331600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:114320400-114337200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:114320600-114331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:114326600-114335000	Weak transcription	Fetal Stomach	stomach
15	chr1:114326600-114335200	Weak transcription	HMEC	breast
16	chr1:114326600-114337800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:114326800-114335200	Weak transcription	HUVEC	blood vessel
18	chr1:114326800-114335800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:114326800-114335800	Weak transcription	NH-A	brain
20	chr1:114326800-114338600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:114326800-114340000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:114327000-114335000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:114327000-114335200	Weak transcription	NHDF-Ad	bronchial
24	chr1:114327000-114336000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:114327000-114337000	Weak transcription	Brain Germinal Matrix	brain
26	chr1:114327200-114331600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:114327200-114331600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:114327200-114331800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:114327200-114332000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:114327200-114333200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:114327200-114334800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:114327200-114337400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:114327400-114331400	Weak transcription	Pancreas	Pancrea
34	chr1:114327400-114331600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr1:114327400-114331600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:114327400-114331600	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:114327400-114331600	Weak transcription	Gastric	stomach
38	chr1:114327400-114331600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:114327400-114331600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:114327400-114331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:114327400-114331800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:114327400-114331800	Weak transcription	Left Ventricle	heart
43	chr1:114327400-114331800	Weak transcription	Lung	lung
44	chr1:114327400-114331800	Weak transcription	Ovary	ovary
45	chr1:114327400-114331800	Weak transcription	Right Atrium	heart
46	chr1:114327400-114331800	Weak transcription	Right Ventricle	heart
47	chr1:114327400-114332000	Weak transcription	HSMM	muscle
48	chr1:114327400-114332000	Weak transcription	NHEK	skin
49	chr1:114327400-114335000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:114327400-114335200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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