Variant report

Variant	rs1295645
Chromosome Location	chr1:227059037-227059038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:
2	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADCK3-4	chr1:227058564-227059105	NONHSAT009905

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10799368	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916039	0.90[JPT][hapmap]
rs10916054	0.92[EUR][1000 genomes]
rs11405	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1150895	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150896	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590925	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12039247	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126209	0.90[EUR][1000 genomes]
rs12128150	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130758	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12131495	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133772	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133818	0.89[EUR][1000 genomes]
rs12563993	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12749910	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1295642	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295646	0.80[EUR][1000 genomes]
rs1295648	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1295651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1297990	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1800678	0.92[CEU][hapmap]
rs2236913	0.92[CEU][hapmap]
rs2802267	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2855563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34741989	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61837761	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61837762	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61837763	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426542	0.86[EUR][1000 genomes]
rs6426543	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426545	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426546	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660109	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6660716	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6663555	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6678134	0.89[EUR][1000 genomes]
rs743602	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7525811	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553957	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs835661	1.00[LWK][hapmap]
rs9660802	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1295645	LEFTY1	cis	cerebellum	SCAN
rs1295645	GJC2	cis	parietal	SCAN
rs1295645	PYCR2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227057600-227059200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:227057800-227059200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:227057800-227059200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:227057800-227059200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:227057800-227059200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr1:227057800-227059200	Active TSS	Fetal Brain Female	brain
7	chr1:227057800-227059200	Active TSS	Left Ventricle	heart
8	chr1:227057800-227059200	Active TSS	Right Atrium	heart
9	chr1:227057800-227059600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:227057800-227059800	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr1:227057800-227060600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:227058000-227059200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:227058000-227059200	Active TSS	Gastric	stomach
14	chr1:227058000-227059200	Active TSS	A549	lung
15	chr1:227058000-227059400	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr1:227058000-227059400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr1:227058000-227059400	Enhancers	Fetal Brain Male	brain
18	chr1:227058600-227059200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:227058600-227059200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
20	chr1:227058600-227059200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr1:227058600-227059200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:227058600-227059400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:227058600-227059400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr1:227058600-227059400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:227058600-227059400	Flanking Active TSS	Osteobl	bone
26	chr1:227058600-227059600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:227058600-227059600	Flanking Active TSS	Colonic Mucosa	Colon
28	chr1:227058600-227059800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr1:227058600-227060000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:227058600-227060000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:227058800-227059200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:227058800-227059200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:227058800-227059200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:227058800-227059200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:227058800-227059200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr1:227058800-227059200	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr1:227058800-227059200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:227058800-227059200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:227058800-227059200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
40	chr1:227058800-227059200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:227058800-227059200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:227058800-227059200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr1:227058800-227059200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:227058800-227059200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:227058800-227059200	Flanking Active TSS	Placenta	Placenta
46	chr1:227058800-227059200	Flanking Active TSS	Lung	lung
47	chr1:227058800-227059200	Flanking Bivalent TSS/Enh	Thymus	Thymus
48	chr1:227058800-227059200	Flanking Active TSS	HUVEC	blood vessel
49	chr1:227058800-227059200	Flanking Active TSS	NH-A	brain
50	chr1:227058800-227059400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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