Variant report

Variant	rs7554177
Chromosome Location	chr1:45305110-45305111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
3	chr1:45239193..45241536-chr1:45303716..45305875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225721	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000142937	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10158188	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465818	0.86[GIH][hapmap]
rs11211037	0.92[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs11211044	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211046	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211047	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11573543	0.83[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs11577974	0.82[JPT][hapmap]
rs11584031	0.92[CEU][hapmap]
rs12059964	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs12094007	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12118515	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12120470	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144803	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408818	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568071	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568279	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][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]
rs2273940	0.91[EUR][1000 genomes]
rs263956	0.87[ASN][1000 genomes]
rs263962	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs263965	0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs263966	0.97[CHD][hapmap]
rs263975	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263977	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs263990	0.97[CHD][hapmap]
rs264011	0.97[CHD][hapmap]
rs3795720	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]
rs452989	0.97[CHD][hapmap]
rs6429548	0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs6688465	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696675	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6698951	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs746320	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514741	0.90[EUR][1000 genomes]
rs7525308	0.92[CEU][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs7526786	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545808	0.91[EUR][1000 genomes]
rs932691	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9645347	0.91[EUR][1000 genomes]
rs9988451	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv532505	chr1:45303803-45307152	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7554177	EIF2B3	cis	cerebellum	SCAN
rs7554177	CTPS	cis	cerebellum	SCAN
rs7554177	EIF2B3	cis	parietal	SCAN
rs7554177	C1orf84	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
2	chr1:45287200-45307400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:45289400-45307600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:45292400-45308200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:45294000-45308200	Weak transcription	Gastric	stomach
6	chr1:45295400-45308400	Weak transcription	Right Ventricle	heart
7	chr1:45295800-45305600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:45295800-45308000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:45296000-45307600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:45297000-45305200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45297000-45305200	Weak transcription	Ovary	ovary
12	chr1:45297400-45305200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:45298000-45305200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:45298000-45305400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:45298000-45308200	Weak transcription	Spleen	Spleen
16	chr1:45298200-45305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:45298800-45308200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:45301800-45305200	Weak transcription	Fetal Lung	lung
19	chr1:45301800-45307400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:45302000-45305200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:45302000-45305200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:45302000-45305200	Weak transcription	Fetal Brain Male	brain
23	chr1:45302000-45306400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:45302000-45307200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:45302000-45307400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:45302000-45307400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:45302000-45307600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:45302000-45307600	Weak transcription	K562	blood
29	chr1:45302000-45308200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:45302000-45308200	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:45302000-45308200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:45302000-45308200	Weak transcription	NHDF-Ad	bronchial
33	chr1:45302000-45308200	Weak transcription	Osteobl	bone
34	chr1:45302000-45308400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:45302000-45308400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:45302000-45308400	Weak transcription	HUVEC	blood vessel
37	chr1:45302200-45305200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:45302200-45305200	Weak transcription	Fetal Brain Female	brain
39	chr1:45302200-45307200	Weak transcription	Brain Angular Gyrus	brain
40	chr1:45302200-45308200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:45302400-45307600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:45302400-45308400	Weak transcription	Right Atrium	heart
43	chr1:45302600-45307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:45302800-45307800	Weak transcription	Fetal Kidney	kidney
45	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:45302800-45308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:45302800-45308200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:45303200-45308200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:45303800-45305400	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:45303800-45305600	Enhancers	HepG2	liver

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