Variant report

Variant	rs712062
Chromosome Location	chr1:225756293-225756294
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225746985..225751093-chr1:225752796..225757571,6	MCF-7	breast:
2	chr1:225754769..225757608-chr1:225839497..225842877,3	MCF-7	breast:
3	chr1:225754514..225756572-chr1:225964591..225966277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10753406	0.89[EUR][1000 genomes]
rs10799311	0.83[EUR][1000 genomes]
rs10799314	0.82[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs10799317	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799318	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.82[EUR][1000 genomes]
rs10915833	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10915834	0.87[EUR][1000 genomes]
rs10915837	0.81[ASN][1000 genomes]
rs10915839	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584675	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12028305	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs12729655	0.81[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2639712	0.82[LWK][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2639716	0.88[EUR][1000 genomes]
rs2657564	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs2840958	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs3820226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856156	0.89[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs476540	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510293	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511649	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516249	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551996	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561656	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426076	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6668770	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676201	0.81[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7515907	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515963	0.81[ASN][1000 genomes]
rs7524766	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7540181	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541598	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555139	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs812523	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947034	0.81[EUR][1000 genomes]
rs9804142	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs712062	MIXL1	cis	cerebellum	SCAN
rs712062	LBR	cis	Artery Tibial	GTEx
rs712062	C1orf58	cis	parietal	SCAN
rs712062	RP11-496N12.9	cis	Thyroid	GTEx
rs712062	PYCR2	cis	cerebellum	SCAN
rs712062	DUSP10	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225717800-225758200	Weak transcription	HepG2	liver
2	chr1:225718400-225756400	Weak transcription	NHLF	lung
3	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
5	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
8	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:225741800-225758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:225744800-225759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:225744800-225760200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:225744800-225761400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
15	chr1:225745000-225760800	Weak transcription	Fetal Kidney	kidney
16	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
17	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
18	chr1:225746600-225756400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:225747200-225759800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:225747800-225756400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:225747800-225765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:225748400-225759800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:225748800-225765800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:225750000-225758000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:225750800-225761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:225751800-225759800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:225752200-225758800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:225753600-225758000	Weak transcription	Fetal Intestine Small	intestine
31	chr1:225753600-225758800	Weak transcription	Lung	lung
32	chr1:225753800-225759200	Weak transcription	Psoas Muscle	Psoas
33	chr1:225754000-225759600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:225754000-225764600	Weak transcription	Fetal Stomach	stomach
35	chr1:225754200-225756400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:225754200-225756400	Weak transcription	A549	lung
37	chr1:225754200-225756600	Weak transcription	NHEK	skin
38	chr1:225754200-225757800	Weak transcription	Hela-S3	cervix
39	chr1:225754200-225761000	Weak transcription	Aorta	Aorta
40	chr1:225754200-225764400	Weak transcription	Right Atrium	heart
41	chr1:225754200-225764600	Weak transcription	Ovary	ovary
42	chr1:225754400-225756400	Weak transcription	NHDF-Ad	bronchial
43	chr1:225754400-225760000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:225754400-225764400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:225754400-225769400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:225754600-225761200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:225754600-225764400	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:225754600-225766000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:225754800-225759800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:225754800-225760200	Weak transcription	NH-A	brain

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