Variant report

Variant	rs4243046
Chromosome Location	chr15:77834746-77834747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77777712..77780447-chr15:77832272..77835232,2	MCF-7	breast:
2	chr15:77828874..77831053-chr15:77833422..77835199,2	MCF-7	breast:
3	chr15:77793530..77795240-chr15:77834025..77836291,2	MCF-7	breast:
4	chr15:77824813..77828626-chr15:77832957..77835709,3	K562	blood:
5	chr15:77829651..77831982-chr15:77834371..77837022,2	MCF-7	breast:
6	chr15:77819974..77827062-chr15:77831334..77836599,8	MCF-7	breast:
7	chr15:77833246..77835948-chr15:77846373..77848114,2	MCF-7	breast:
8	chr15:77795040..77797177-chr15:77834449..77837320,2	MCF-7	breast:
9	chr15:77833855..77835939-chr15:77840027..77842265,2	K562	blood:
10	chr15:77412894..77414915-chr15:77833378..77835255,2	K562	blood:
11	chr15:77795420..77798597-chr15:77834386..77837370,5	MCF-7	breast:
12	chr15:77827126..77831240-chr15:77834209..77836612,4	K562	blood:
13	chr15:77822048..77824496-chr15:77832446..77834927,2	K562	blood:

No data

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11855272	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1317320	0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs16953967	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16968893	0.86[ASN][1000 genomes]
rs16968895	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16968897	0.81[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs16968900	0.82[EUR][1000 genomes]
rs16968930	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17394448	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs2137111	0.89[JPT][hapmap];0.86[MEX][hapmap]
rs28375490	0.91[EUR][1000 genomes]
rs28534698	0.89[EUR][1000 genomes]
rs2867303	0.85[ASN][1000 genomes]
rs28712147	0.92[EUR][1000 genomes]
rs4886870	0.82[ASN][1000 genomes]
rs4886874	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61097729	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61483316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74026930	0.86[ASN][1000 genomes]
rs74026931	0.86[ASN][1000 genomes]
rs74026932	0.86[ASN][1000 genomes]
rs74026933	0.86[ASN][1000 genomes]
rs907370	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs907371	0.95[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs907387	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
5	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4243046	CYP1A2	cis	cerebellum	SCAN
rs4243046	STRA6	cis	cerebellum	SCAN
rs4243046	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs4243046	TSPAN3	cis	cerebellum	SCAN
rs4243046	HMG20A	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77827000-77835400	Weak transcription	Psoas Muscle	Psoas
2	chr15:77827000-77845400	Weak transcription	Fetal Kidney	kidney
3	chr15:77828400-77835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77828400-77835400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr15:77828400-77835400	Enhancers	Brain Anterior Caudate	brain
6	chr15:77829400-77835000	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:77829400-77844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:77829600-77835400	Enhancers	Fetal Stomach	stomach
9	chr15:77829800-77835400	Enhancers	Fetal Brain Female	brain
10	chr15:77830000-77835200	Enhancers	Fetal Muscle Leg	muscle
11	chr15:77831200-77835000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:77831400-77835200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr15:77831600-77835000	Enhancers	Spleen	Spleen
14	chr15:77831600-77835200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:77831800-77835200	Weak transcription	Ovary	ovary
16	chr15:77832000-77835000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:77832000-77835400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:77832200-77834800	Weak transcription	Gastric	stomach
19	chr15:77832200-77835200	Weak transcription	Fetal Thymus	thymus
20	chr15:77832400-77835000	Weak transcription	Pancreas	Pancrea
21	chr15:77832600-77835200	Enhancers	Brain Germinal Matrix	brain
22	chr15:77832600-77835400	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:77832600-77835400	Enhancers	Placenta	Placenta
24	chr15:77832800-77835000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr15:77832800-77835400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:77832800-77835400	Enhancers	Right Ventricle	heart
27	chr15:77832800-77836000	Enhancers	NHDF-Ad	bronchial
28	chr15:77833000-77835000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:77833000-77835000	Weak transcription	Lung	lung
30	chr15:77833000-77835200	Enhancers	Brain Angular Gyrus	brain
31	chr15:77833000-77835200	Enhancers	Brain Hippocampus Middle	brain
32	chr15:77833000-77835600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr15:77833000-77836600	Enhancers	Fetal Brain Male	brain
34	chr15:77833200-77834800	Weak transcription	GM12878-XiMat	blood
35	chr15:77833200-77835000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:77833200-77835200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:77833200-77836200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:77833400-77835000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:77833400-77835200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:77833400-77835200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:77833600-77834800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:77833600-77835000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:77833600-77835000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:77833600-77835000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr15:77833600-77835000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:77833600-77835200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:77833600-77835200	Enhancers	Colonic Mucosa	Colon
48	chr15:77833600-77835400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:77833600-77835400	Enhancers	Right Atrium	heart
50	chr15:77833800-77834800	Weak transcription	Rectal Mucosa Donor 29	rectum

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