Variant report

Variant	rs4845623
Chromosome Location	chr1:154415777-154415778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154413948..154418058-chr1:154421616..154424516,3	MCF-7	breast:
2	chr1:154414588..154416546-chr1:154448223..154449736,2	K562	blood:
3	chr1:154415046..154417518-chr1:154446987..154449736,2	K562	blood:
4	chr1:154409978..154411653-chr1:154414842..154417347,2	MCF-7	breast:
5	chr1:154406170..154408032-chr1:154413568..154416064,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11265612	0.83[AFR][1000 genomes]
rs11265613	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126142	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12133641	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12730036	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730935	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12753254	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228145	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129267	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133213	0.90[ASN][1000 genomes]
rs4393147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4537545	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4576655	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845371	0.94[ASW][hapmap];0.84[LWK][hapmap];0.82[YRI][hapmap]
rs4845372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845373	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845620	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845621	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845625	0.89[ASW][hapmap];0.80[LWK][hapmap]
rs56383622	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61812598	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6427658	0.87[ASW][hapmap]
rs6664201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667434	0.81[YRI][hapmap];0.80[AFR][1000 genomes]
rs6684439	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689393	0.89[ASW][hapmap];0.80[LWK][hapmap]
rs6694817	0.94[ASW][hapmap]
rs7512646	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518199	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7521458	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529229	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4845623	LINGO4	cis	parietal	SCAN
rs4845623	ANXA9	cis	parietal	SCAN
rs4845623	LYSMD1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
3	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
5	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:154407400-154416200	Genic enhancers	Liver	Liver
7	chr1:154407400-154417400	Weak transcription	Brain Anterior Caudate	brain
8	chr1:154407600-154417200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:154407600-154418600	Weak transcription	Ovary	ovary
10	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
12	chr1:154408800-154416000	Weak transcription	Right Ventricle	heart
13	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:154409200-154417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:154409200-154420600	Weak transcription	Gastric	stomach
19	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
20	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
21	chr1:154410400-154418000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:154410600-154415800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:154410800-154418600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:154410800-154418800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:154411400-154416000	Weak transcription	Left Ventricle	heart
26	chr1:154412400-154415800	Enhancers	Fetal Thymus	thymus
27	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
28	chr1:154412800-154417000	Weak transcription	Fetal Intestine Small	intestine
29	chr1:154412800-154425800	Weak transcription	HepG2	liver
30	chr1:154413000-154419600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:154413400-154415800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:154413400-154417800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:154413600-154415800	Enhancers	HMEC	breast
35	chr1:154413600-154418800	Genic enhancers	Colon Smooth Muscle	Colon
36	chr1:154413600-154419600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:154413800-154416600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:154413800-154418800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:154414000-154416800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:154414200-154415800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:154414200-154416000	Enhancers	Osteobl	bone
42	chr1:154414400-154416000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:154414400-154416200	Enhancers	NHLF	lung
44	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:154414600-154418000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
49	chr1:154414800-154415800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:154414800-154416000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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