Variant report

Variant	rs6495069
Chromosome Location	chr15:73878570-73878571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73877183..73878690-chr15:73881070..73882609,2	MCF-7	breast:
2	chr15:73877125..73879241-chr15:73920215..73923156,2	K562	blood:
3	chr15:73877182..73878738-chr15:73883851..73886514,2	K562	blood:
4	chr15:73875024..73876650-chr15:73877953..73880121,2	MCF-7	breast:
5	chr15:73870692..73873322-chr15:73878478..73880612,2	MCF-7	breast:
6	chr15:73877093..73883736-chr15:73923951..73929327,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10851863	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072429	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11072430	0.80[JPT][hapmap]
rs11072431	0.80[JPT][hapmap]
rs12148532	0.86[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12148719	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12185108	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442903	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12593246	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1383616	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1481088	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1481089	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16958079	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17185294	0.81[TSI][hapmap]
rs3743500	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4470111	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4558379	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6495075	0.80[JPT][hapmap]
rs6495076	0.82[JPT][hapmap]
rs7169374	0.82[ASN][1000 genomes]
rs7176637	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8023823	0.87[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs8028089	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8037836	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs922687	0.90[ASN][1000 genomes]
rs9920359	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6495069	LMAN1L	cis	parietal	SCAN
rs6495069	ARIH1	cis	cerebellum	SCAN
rs6495069	FEZ1	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73847400-73893200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:73847600-73882400	Strong transcription	Placenta	Placenta
3	chr15:73848800-73884800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:73848800-73885000	Strong transcription	Primary B cells from cord blood	blood
5	chr15:73850200-73884400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:73857400-73884800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:73857600-73885000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:73858000-73884800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:73858200-73885800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:73859400-73882000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:73860600-73885000	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:73862200-73884800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr15:73863200-73889400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:73863800-73882000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:73866800-73884800	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:73867800-73884400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:73870000-73884400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr15:73870200-73879400	Strong transcription	NHDF-Ad	bronchial
19	chr15:73870200-73881600	Strong transcription	Brain Hippocampus Middle	brain
20	chr15:73870200-73884600	Strong transcription	HepG2	liver
21	chr15:73870400-73887000	Strong transcription	Primary T cells from cord blood	blood
22	chr15:73871400-73884600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:73871600-73884200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:73871600-73884400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:73871600-73884600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:73871600-73884600	Strong transcription	HMEC	breast
27	chr15:73871600-73886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:73871600-73886400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:73871600-73887400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:73871800-73882200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:73871800-73882800	Strong transcription	Liver	Liver
32	chr15:73871800-73883600	Strong transcription	Left Ventricle	heart
33	chr15:73871800-73884400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr15:73871800-73884600	Strong transcription	Fetal Lung	lung
35	chr15:73871800-73884800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:73872000-73881200	Strong transcription	Fetal Brain Female	brain
37	chr15:73872000-73884200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:73872000-73884400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:73872000-73884800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr15:73872400-73880400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:73872800-73880200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr15:73872800-73880400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:73872800-73884400	Strong transcription	Adipose Nuclei	Adipose
44	chr15:73872800-73884600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:73873000-73884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:73873000-73884600	Strong transcription	Thymus	Thymus
47	chr15:73873200-73884600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr15:73873200-73884600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:73873200-73884600	Strong transcription	NH-A	brain
50	chr15:73873200-73888800	Strong transcription	NHEK	skin

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