Variant report

Variant	rs3795720
Chromosome Location	chr1:45307506-45307507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
2	chr1:45306094..45308477-chr1:45314879..45317391,2	K562	blood:
3	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
4	chr1:45194535..45197095-chr1:45307118..45309179,4	K562	blood:
5	chr1:45195257..45196854-chr1:45307118..45309179,2	K562	blood:
6	chr1:45185746..45188870-chr1:45307191..45310438,4	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10158188	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465818	0.94[GIH][hapmap]
rs11211030	0.81[GIH][hapmap]
rs11211031	0.81[GIH][hapmap]
rs11211037	0.96[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap]
rs11211044	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211047	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11573543	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[ASN][1000 genomes]
rs11577974	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs11584031	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs12059964	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.80[ASN][1000 genomes]
rs12094007	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120470	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12136048	0.81[GIH][hapmap]
rs12144803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568279	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273940	0.92[EUR][1000 genomes]
rs263956	0.87[ASN][1000 genomes]
rs263962	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263965	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs263966	0.97[CHD][hapmap];0.86[GIH][hapmap]
rs263975	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263977	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263990	0.97[CHD][hapmap]
rs264011	0.97[CHD][hapmap];0.80[GIH][hapmap]
rs452989	0.97[CHD][hapmap];0.80[GIH][hapmap]
rs6429548	0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap]
rs6688465	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698951	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514741	0.90[EUR][1000 genomes]
rs7524446	0.81[CHB][hapmap]
rs7525308	0.96[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs7526786	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7536146	0.81[GIH][hapmap]
rs7545808	0.92[EUR][1000 genomes]
rs7554177	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932691	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9645347	0.92[EUR][1000 genomes]
rs9988451	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
9	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3795720	C1orf84	cis	parietal	SCAN
rs3795720	CTPS	cis	cerebellum	SCAN
rs3795720	EIF2B3	cis	parietal	SCAN
rs3795720	EIF2B3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
2	chr1:45289400-45307600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:45292400-45308200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:45294000-45308200	Weak transcription	Gastric	stomach
5	chr1:45295400-45308400	Weak transcription	Right Ventricle	heart
6	chr1:45295800-45308000	Weak transcription	Brain Germinal Matrix	brain
7	chr1:45296000-45307600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:45298000-45308200	Weak transcription	Spleen	Spleen
9	chr1:45298800-45308200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45302000-45307600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:45302000-45307600	Weak transcription	K562	blood
12	chr1:45302000-45308200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:45302000-45308200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:45302000-45308200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:45302000-45308200	Weak transcription	NHDF-Ad	bronchial
16	chr1:45302000-45308200	Weak transcription	Osteobl	bone
17	chr1:45302000-45308400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:45302000-45308400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:45302000-45308400	Weak transcription	HUVEC	blood vessel
20	chr1:45302200-45308200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:45302400-45307600	Weak transcription	Fetal Intestine Small	intestine
22	chr1:45302400-45308400	Weak transcription	Right Atrium	heart
23	chr1:45302800-45307800	Weak transcription	Fetal Kidney	kidney
24	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:45302800-45308200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:45303200-45308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:45305600-45308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:45305800-45307600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:45305800-45308400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:45307000-45307600	Enhancers	Fetal Brain Male	brain
32	chr1:45307200-45307800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:45307200-45307800	Enhancers	Fetal Lung	lung
34	chr1:45307200-45308000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:45307200-45308200	Enhancers	Brain Angular Gyrus	brain
36	chr1:45307400-45307600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:45307400-45307600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:45307400-45307600	Enhancers	Colonic Mucosa	Colon
39	chr1:45307400-45307800	Flanking Active TSS	Fetal Muscle Leg	muscle
40	chr1:45307400-45307800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
41	chr1:45307400-45307800	Flanking Active TSS	Ovary	ovary
42	chr1:45307400-45307800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr1:45307400-45308200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:45307400-45308200	Enhancers	Brain Anterior Caudate	brain
45	chr1:45307400-45308200	Enhancers	Colon Smooth Muscle	Colon
46	chr1:45307400-45308200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:45307400-45308400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:45307400-45308400	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr1:45307400-45308600	Flanking Active TSS	Fetal Brain Female	brain
50	chr1:45307400-45308600	Flanking Active TSS	HepG2	liver

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