Variant report

Variant	rs710130
Chromosome Location	chr1:10607394-10607395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10591516..10593262-chr1:10606474..10609056,2	K562	blood:
2	chr1:10586788..10588823-chr1:10605231..10607555,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10157111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10157119	0.99[ASN][1000 genomes]
rs10746495	0.98[ASN][1000 genomes]
rs10779739	0.99[ASN][1000 genomes]
rs10779743	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779744	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10864463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs11121584	0.98[ASN][1000 genomes]
rs11121585	0.93[ASN][1000 genomes]
rs11121588	0.99[ASN][1000 genomes]
rs11121589	0.99[ASN][1000 genomes]
rs11121593	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12033275	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12128630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12133103	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565494	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12750901	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12753364	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039175	0.95[ASN][1000 genomes]
rs2039176	0.98[ASN][1000 genomes]
rs2086650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2480771	0.99[ASN][1000 genomes]
rs2480772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs2480773	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs2480775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2480780	0.90[JPT][hapmap]
rs2480781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2480789	0.85[LWK][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs2506878	0.85[JPT][hapmap]
rs2506888	0.83[YRI][hapmap]
rs2506897	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2506898	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2506900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2988398	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34230252	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35409029	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35612158	0.99[ASN][1000 genomes]
rs4240914	0.90[JPT][hapmap]
rs4240915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs4617401	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845936	0.98[ASN][1000 genomes]
rs4846230	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs4846231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4846232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4846233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4846237	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61777207	0.99[ASN][1000 genomes]
rs61777208	0.99[ASN][1000 genomes]
rs6540937	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540938	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6661757	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664134	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687502	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687622	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700023	0.98[ASN][1000 genomes]
rs6700886	0.95[ASN][1000 genomes]
rs747124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7512467	0.93[CHD][hapmap];0.90[JPT][hapmap]
rs7519424	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524790	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7534954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536149	0.88[EUR][1000 genomes]
rs944191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9660006	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs9661121	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs710130	FBXO44	cis	parietal	SCAN
rs710130	MTHFR	cis	parietal	SCAN
rs710130	PEX14	cis	multi-tissue	Pritchard
rs710130	Hs.211939	cis	multi-tissue	Pritchard
rs710130	PEX14	cis	Lymphoblastoid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
3	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
4	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
5	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:10598600-10621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:10599800-10608400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:10599800-10610000	Weak transcription	Stomach Mucosa	stomach
11	chr1:10600000-10608200	Weak transcription	Fetal Brain Male	brain
12	chr1:10600000-10615600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:10600000-10615800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:10600000-10619600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:10600200-10614800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:10600200-10615800	Weak transcription	HSMM	muscle
17	chr1:10601000-10607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:10601000-10613000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:10601200-10613400	Weak transcription	Osteobl	bone
20	chr1:10601200-10619600	Weak transcription	Brain Anterior Caudate	brain
21	chr1:10601400-10610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:10601400-10611000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:10601400-10611000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:10601400-10615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:10601800-10610000	Weak transcription	Fetal Lung	lung
26	chr1:10601800-10610000	Weak transcription	A549	lung
27	chr1:10601800-10610000	Weak transcription	HUVEC	blood vessel
28	chr1:10601800-10613200	Weak transcription	K562	blood
29	chr1:10601800-10613400	Weak transcription	Right Ventricle	heart
30	chr1:10602000-10608400	Weak transcription	Fetal Heart	heart
31	chr1:10602000-10609800	Weak transcription	Colonic Mucosa	Colon
32	chr1:10602000-10610000	Weak transcription	Gastric	stomach
33	chr1:10602000-10610200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:10602000-10610200	Weak transcription	HepG2	liver
35	chr1:10602000-10610600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:10602000-10610800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:10602000-10610800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:10602000-10611400	Weak transcription	Ovary	ovary
39	chr1:10602000-10612800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:10602000-10612800	Weak transcription	Fetal Thymus	thymus
41	chr1:10602000-10613000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:10602000-10613200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:10602000-10615600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:10602000-10615600	Weak transcription	HMEC	breast
45	chr1:10602000-10616200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:10602000-10619400	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:10602000-10639600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:10602200-10609600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:10602200-10615600	Weak transcription	Placenta	Placenta
50	chr1:10602200-10615600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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