Variant report

Variant	rs1548505
Chromosome Location	chr19:36586776-36586777
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	chr19:36586278..36587946-chr19:36591359..36594348,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1003470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420353	0.85[YRI][hapmap]
rs10421966	0.91[YRI][hapmap]
rs10853945	1.00[ASN][1000 genomes]
rs12462674	0.87[YRI][hapmap]
rs12980591	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982375	0.99[ASN][1000 genomes]
rs1548506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1972511	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985404	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023865	0.87[YRI][hapmap]
rs2051800	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2072605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2239510	0.82[YRI][hapmap]
rs2285745	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2301736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2311004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746271	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826995	0.87[YRI][hapmap]
rs4461192	0.86[YRI][hapmap]
rs4805160	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4806265	0.90[ASN][1000 genomes]
rs4806269	0.95[ASN][1000 genomes]
rs4806270	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510519	0.86[ASN][1000 genomes]
rs7246292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757223	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8103569	0.87[YRI][hapmap]

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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1548505	CYP2B7P1	cis	parietal	SCAN
rs1548505	ATXN7L1	trans	parietal	SCAN
rs1548505	ZNF229	cis	parietal	SCAN
rs1548505	GRIK5	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
2	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
8	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
9	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:36561200-36597600	Strong transcription	Dnd41	blood
13	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:36562000-36588600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:36563000-36594200	Weak transcription	HSMM	muscle
20	chr19:36566000-36592000	Weak transcription	HMEC	breast
21	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:36568800-36594800	Strong transcription	A549	lung
23	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
25	chr19:36571600-36596600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr19:36571800-36588400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr19:36571800-36588600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:36571800-36591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:36571800-36598400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
32	chr19:36572000-36598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:36572200-36588200	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:36572400-36588400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:36572400-36588400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:36573800-36602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:36574200-36593600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:36574200-36602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:36574400-36592600	Weak transcription	HUVEC	blood vessel
41	chr19:36574600-36604400	Weak transcription	NHDF-Ad	bronchial
42	chr19:36574800-36587800	Weak transcription	NH-A	brain
43	chr19:36575400-36604200	Weak transcription	Primary B cells from cord blood	blood
44	chr19:36580000-36590400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:36580400-36594800	Weak transcription	Primary T cells from cord blood	blood
46	chr19:36581200-36593600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr19:36581600-36590200	Weak transcription	Fetal Brain Female	brain
48	chr19:36581600-36592200	Weak transcription	Fetal Intestine Large	intestine
49	chr19:36581800-36594200	Weak transcription	K562	blood
50	chr19:36582200-36590200	Weak transcription	Spleen	Spleen

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