Variant report

Variant	rs11856084
Chromosome Location	chr15:77750410-77750411
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:77749533-77750694	HUVEC	blood vessel:	n/a	n/a
2	MAX	chr15:77749980-77750554	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr15:77749838-77751238	SK-N-SH	brain:	n/a	n/a
4	MAFK	chr15:77750231-77750463	HepG2	liver:	n/a	chr15:77750336-77750351
5	TCF12	chr15:77749659-77751359	SK-N-SH	brain:	n/a	n/a
6	FOS	chr15:77749491-77750949	HUVEC	blood vessel:	n/a	chr15:77749707-77749716 chr15:77750153-77750162
7	JUN	chr15:77749782-77750577	HUVEC	blood vessel:	n/a	chr15:77750153-77750162
8	GATA3	chr15:77749605-77751303	SK-N-SH	brain:	n/a	chr15:77750544-77750560 chr15:77750549-77750559 chr15:77750447-77750457 chr15:77750153-77750163 chr15:77750732-77750742 chr15:77751251-77751258
9	MAFK	chr15:77750074-77750537	IMR90	lung:	n/a	chr15:77750336-77750351
10	FOSL2	chr15:77749881-77750691	SK-N-SH	brain:	n/a	chr15:77750153-77750162
11	GATA3	chr15:77749714-77751133	SK-N-SH	brain:	n/a	chr15:77750544-77750560 chr15:77750549-77750559 chr15:77750447-77750457 chr15:77750153-77750163 chr15:77750732-77750742
12	PBX3	chr15:77749678-77751194	SK-N-SH	brain:	n/a	chr15:77750969-77750978
13	MAFK	chr15:77750179-77750504	HepG2	liver:	n/a	chr15:77750336-77750351
14	MAFF	chr15:77750198-77750490	HepG2	liver:	n/a	chr15:77750335-77750353
15	POLR2A	chr15:77750294-77750552	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr15:77750223-77751279	SK-N-SH	brain:	n/a	chr15:77750969-77750978
17	GATA2	chr15:77749563-77750986	HUVEC	blood vessel:	n/a	chr15:77750544-77750560 chr15:77750549-77750559 chr15:77750447-77750457 chr15:77750153-77750163 chr15:77750732-77750742

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77712015..77714153-chr15:77749765..77751911,2	MCF-7	breast:

Variant related genes	Relation type
HMG20A	TF binding region
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10162742	0.85[YRI][hapmap]
rs11853696	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs11858844	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12324016	0.83[ASN][1000 genomes]
rs12324211	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12324632	0.87[YRI][hapmap]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912084	0.84[ASN][1000 genomes]
rs13380202	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493699	0.83[ASN][1000 genomes]
rs16968799	0.83[ASN][1000 genomes]
rs16968897	0.90[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16968900	0.80[EUR][1000 genomes]
rs16968930	0.82[JPT][hapmap]
rs17384809	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385059	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17385352	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17470529	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17470952	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471252	0.87[ASN][1000 genomes]
rs17471431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471480	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17471753	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17472200	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137111	0.82[JPT][hapmap]
rs2172587	0.83[ASN][1000 genomes]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437977	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35651077	0.83[ASN][1000 genomes]
rs3784787	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4592615	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs4886863	0.84[ASN][1000 genomes]
rs4886864	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886865	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886874	0.82[JPT][hapmap]
rs56097641	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59204923	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs59362734	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59386622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61306472	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62007297	0.86[ASN][1000 genomes]
rs62010566	0.83[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap]
rs74026910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74026912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026913	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026918	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74026923	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74026925	0.95[EUR][1000 genomes]
rs74026926	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8035526	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883627	0.94[JPT][hapmap]
rs907371	0.82[JPT][hapmap]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11856084	CYP1A2	cis	cerebellum	SCAN
rs11856084	STRA6	cis	cerebellum	SCAN
rs11856084	HMG20A	cis	parietal	SCAN
rs11856084	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77717000-77754400	Weak transcription	K562	blood
2	chr15:77730600-77758800	Weak transcription	Lung	lung
3	chr15:77736800-77750800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:77738600-77750600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:77739000-77750800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:77739800-77750800	Weak transcription	Liver	Liver
7	chr15:77739800-77751800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:77739800-77755600	Weak transcription	A549	lung
9	chr15:77740000-77750600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:77740200-77751800	Weak transcription	Brain Angular Gyrus	brain
11	chr15:77741000-77756000	Weak transcription	Colonic Mucosa	Colon
12	chr15:77742400-77750800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:77743200-77750800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:77743200-77751400	Weak transcription	Hela-S3	cervix
15	chr15:77743200-77763200	Weak transcription	Brain Germinal Matrix	brain
16	chr15:77743400-77750600	Weak transcription	Primary B cells from cord blood	blood
17	chr15:77744000-77750600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:77744000-77750800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:77746000-77751000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:77746200-77751000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:77746400-77750600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:77746600-77751200	Enhancers	Fetal Lung	lung
23	chr15:77747000-77750600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr15:77747000-77751200	Enhancers	NH-A	brain
25	chr15:77747200-77750600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr15:77747200-77750800	Enhancers	Adipose Nuclei	Adipose
27	chr15:77747200-77751200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr15:77747200-77751200	Enhancers	NHLF	lung
29	chr15:77747400-77750800	Enhancers	HSMM	muscle
30	chr15:77747600-77751800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:77747800-77750600	Enhancers	Fetal Kidney	kidney
32	chr15:77747800-77751400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr15:77748000-77750600	Enhancers	Colon Smooth Muscle	Colon
34	chr15:77748000-77750600	Enhancers	Small Intestine	intestine
35	chr15:77748000-77750600	Enhancers	Dnd41	blood
36	chr15:77748000-77751000	Enhancers	Fetal Stomach	stomach
37	chr15:77748000-77751000	Enhancers	Stomach Mucosa	stomach
38	chr15:77748200-77750800	Weak transcription	Fetal Brain Female	brain
39	chr15:77748200-77751600	Enhancers	NHDF-Ad	bronchial
40	chr15:77748200-77766800	Weak transcription	Aorta	Aorta
41	chr15:77748400-77750600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:77748400-77750800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:77748400-77770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:77748600-77751000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:77748800-77751000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:77748800-77751000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:77748800-77751000	Enhancers	Osteobl	bone
48	chr15:77749000-77750800	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:77749000-77750800	Weak transcription	Placenta	Placenta
50	chr15:77749000-77757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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