Variant report

Variant	rs4845626
Chromosome Location	chr1:154423485-154423486
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154413948..154418058-chr1:154421616..154424516,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10159236	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10752642	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs11265618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265627	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs11804305	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023358	0.82[ASN][1000 genomes]
rs12047973	0.84[ASN][1000 genomes]
rs12048091	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048950	0.84[ASN][1000 genomes]
rs14021	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs16836054	1.00[CEU][hapmap]
rs4288587	1.00[CEU][hapmap]
rs4308966	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4329505	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345796	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4474240	1.00[CEU][hapmap];0.83[MEX][hapmap]
rs4518898	1.00[CEU][hapmap]
rs4845374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs55800510	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55826755	0.87[ASN][1000 genomes]
rs57502626	0.87[ASN][1000 genomes]
rs61812592	0.87[ASN][1000 genomes]
rs61812593	0.87[ASN][1000 genomes]
rs61812594	0.87[ASN][1000 genomes]
rs61812596	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61812599	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812626	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427716	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6670375	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6687112	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6691727	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs7513603	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs7539745	1.00[CEU][hapmap]
rs7543174	0.94[CEU][hapmap]
rs7553602	1.00[CEU][hapmap]
rs9427415	1.00[CEU][hapmap];1.00[MEX][hapmap]

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	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
2	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
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4845626	DPM3	cis	cerebellum	SCAN
rs4845626	SNX27	cis	parietal	SCAN
rs4845626	RPTN	cis	cerebellum	SCAN
rs4845626	CHRNB2	cis	parietal	SCAN
rs4845626	SMCP	cis	parietal	SCAN

Chromatin state (count:87 , 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	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
6	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
7	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
8	chr1:154412800-154425800	Weak transcription	HepG2	liver
9	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
13	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:154415200-154424000	Weak transcription	Fetal Stomach	stomach
15	chr1:154415800-154425800	Weak transcription	Esophagus	oesophagus
16	chr1:154416200-154435800	Strong transcription	Liver	Liver
17	chr1:154416600-154424400	Weak transcription	Colonic Mucosa	Colon
18	chr1:154416600-154425600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:154417800-154426000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:154418000-154425600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:154418000-154425800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:154418000-154428000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
25	chr1:154418200-154425000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:154418600-154425400	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:154418600-154432800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:154418800-154425800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:154419000-154424400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:154419000-154425000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:154419200-154425200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:154419200-154425400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:154419200-154425600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:154419200-154425800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:154419200-154425800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:154419200-154427200	Weak transcription	Ovary	ovary
37	chr1:154419200-154432200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:154419400-154425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:154419600-154425600	Weak transcription	Osteobl	bone
41	chr1:154420200-154425000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:154420400-154423600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:154420400-154424800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:154420400-154424800	Strong transcription	Left Ventricle	heart
45	chr1:154420400-154425000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:154420400-154425400	Strong transcription	Primary T cells from cord blood	blood
47	chr1:154420400-154425400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr1:154420400-154425400	Strong transcription	Lung	lung
49	chr1:154420400-154425800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:154420400-154425800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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