Variant report

Variant	rs4845618
Chromosome Location	chr1:154400015-154400016
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154399974-154400086	HepG2	liver:	n/a	n/a
2	MXI1	chr1:154399940-154400096	HepG2	liver:	n/a	n/a
3	TCF7L2	chr1:154399992-154400627	PANC-1	pancreas:	n/a	chr1:154400493-154400509 chr1:154400148-154400162 chr1:154400151-154400160 chr1:154400147-154400163 chr1:154400498-154400505 chr1:154400151-154400161 chr1:154400147-154400163 chr1:154400150-154400159
4	TCF7L2	chr1:154399936-154400435	Hela-S3	cervix:	n/a	chr1:154400148-154400162 chr1:154400151-154400160 chr1:154400147-154400163 chr1:154400151-154400161 chr1:154400147-154400163 chr1:154400150-154400159

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154377513..154380266-chr1:154397854..154400617,3	MCF-7	breast:
2	chr1:154390689..154395033-chr1:154398195..154400850,6	MCF-7	breast:

Variant related genes	Relation type
IL6R	TF binding region
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10908837	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908838	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265611	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11265612	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117832	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118721	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12118770	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4553185	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4601580	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4845371	0.84[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845619	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845625	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs59632925	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667434	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6686750	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6687726	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689306	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6689393	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes]
rs6694258	0.84[AMR][1000 genomes]
rs6694817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549250	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549338	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7553796	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4845618	UBE2Q1	cis	cerebellum	SCAN
rs4845618	LINGO4	cis	parietal	SCAN
rs4845618	TDRD10	cis	lung	GTEx
rs4845618	PI4KB	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154392800-154400200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:154392800-154400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
6	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:154393800-154401200	Enhancers	Hela-S3	cervix
9	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:154394000-154404000	Weak transcription	GM12878-XiMat	blood
12	chr1:154395600-154400200	Weak transcription	Fetal Thymus	thymus
13	chr1:154395600-154401200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:154396800-154401200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:154396800-154401600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:154396800-154402200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:154397000-154400200	Weak transcription	Fetal Kidney	kidney
18	chr1:154397000-154402200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:154397000-154402800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:154397200-154400200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:154397200-154402400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:154397200-154402600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:154397200-154403800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:154397400-154400800	Weak transcription	Primary T cells from cord blood	blood
26	chr1:154397400-154401000	Enhancers	Liver	Liver
27	chr1:154397600-154401600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:154398400-154403400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:154398600-154400800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:154399200-154401000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:154399200-154401600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:154399200-154402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:154399400-154400400	Genic enhancers	Primary monocytes fromperipheralblood	blood
34	chr1:154399400-154400600	Enhancers	NHEK	skin
35	chr1:154399400-154401600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:154399400-154403200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:154399400-154405800	Enhancers	Right Atrium	heart
38	chr1:154399400-154407200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:154399600-154400200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:154399600-154400600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:154399600-154400600	Enhancers	HMEC	breast
42	chr1:154399600-154400800	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:154399600-154401200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:154399600-154401200	Enhancers	Lung	lung
45	chr1:154399600-154401200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr1:154399600-154401200	Enhancers	HepG2	liver
47	chr1:154399600-154401400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:154399600-154401400	Enhancers	Adipose Nuclei	Adipose
49	chr1:154399600-154401400	Enhancers	Colonic Mucosa	Colon
50	chr1:154399600-154401400	Enhancers	Duodenum Smooth Muscle	Duodenum

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