Variant report

Variant	rs8040516
Chromosome Location	chr15:73598548-73598549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73598014..73598904-chr15:73928513..73929048,2	K562	blood:
2	chr15:73598029..73598944-chr15:73992348..73993218,4	K562	blood:
3	chr15:73598023..73598791-chr15:73831624..73832277,2	MCF-7	breast:
4	chr15:73598394..73598898-chr15:73823428..73824292,2	K562	blood:
5	chr15:73597949..73598920-chr15:73928445..73929381,7	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10048053	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1023924	0.81[CHB][hapmap];0.94[CHD][hapmap]
rs10438294	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10467949	0.81[CHD][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs11072406	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11072409	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1131854	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633469	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636241	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11639213	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12050774	0.81[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap]
rs12050848	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12708506	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12902768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907139	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1479338	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1479339	0.81[CHB][hapmap]
rs1479340	0.81[CHD][hapmap]
rs1564345	0.81[CHD][hapmap]
rs17762600	0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs17829830	0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs17829957	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1812835	0.85[CEU][hapmap]
rs1871385	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2046017	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2127277	0.80[CHD][hapmap]
rs2194924	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2251205	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2252725	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2415147	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415148	0.81[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs34013312	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35450875	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736510	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3743489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784793	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3784796	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784801	0.81[CHB][hapmap]
rs4381562	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776630	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4777589	0.81[CHD][hapmap];0.80[GIH][hapmap]
rs4777590	0.94[CHD][hapmap]
rs489531	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs56157337	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62015500	0.95[ASN][1000 genomes]
rs62015502	0.82[ASN][1000 genomes]
rs62017779	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7172021	0.81[CHD][hapmap]
rs7175329	0.81[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap]
rs747872	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs747873	0.82[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8024575	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8027588	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8029106	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035063	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035925	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8042700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs922516	0.81[CHD][hapmap];0.80[GIH][hapmap]
rs9672588	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9972523	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8040516	CYP1A2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
3	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
5	chr15:73585000-73599400	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:73585400-73599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:73586800-73601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:73588600-73598600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:73588800-73601400	Strong transcription	Fetal Intestine Large	intestine
10	chr15:73588800-73601800	Strong transcription	Fetal Intestine Small	intestine
11	chr15:73591400-73598600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:73593200-73601800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:73593200-73602000	Strong transcription	Aorta	Aorta
14	chr15:73593400-73598600	Weak transcription	A549	lung
15	chr15:73595400-73598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:73595400-73600000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:73595400-73603800	Weak transcription	Spleen	Spleen
18	chr15:73595600-73598600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:73595600-73601600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr15:73595600-73610200	Weak transcription	Fetal Brain Male	brain
21	chr15:73596200-73598600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:73596200-73599800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:73596400-73599000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:73596400-73611000	Weak transcription	Brain Anterior Caudate	brain
25	chr15:73596600-73598800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr15:73596600-73599200	Weak transcription	Pancreas	Pancrea
27	chr15:73596600-73610000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:73596600-73610200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:73596800-73598600	Weak transcription	Liver	Liver
30	chr15:73596800-73598600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:73596800-73602200	Weak transcription	Lung	lung
32	chr15:73596800-73609600	Weak transcription	Fetal Lung	lung
33	chr15:73596800-73616800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:73597000-73599200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:73597000-73599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:73597000-73599600	Weak transcription	Fetal Brain Female	brain
37	chr15:73597000-73600000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:73597000-73600000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:73597000-73601000	Weak transcription	Fetal Kidney	kidney
40	chr15:73597000-73601000	Weak transcription	Ovary	ovary
41	chr15:73597000-73606000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:73597000-73609600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:73597000-73610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr15:73597200-73599200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:73597200-73599400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:73597200-73602200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:73597200-73603600	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:73597400-73598600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:73597400-73603200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:73597600-73598800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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