Variant report

Variant	rs907396
Chromosome Location	chr15:77910202-77910203
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77904297..77907501-chr15:77908507..77911725,4	K562	blood:
2	chr15:77835734..77836523-chr15:77909574..77910418,2	MCF-7	breast:
3	chr15:77908000..77910749-chr15:77912406..77914677,2	MCF-7	breast:
4	chr15:77898597..77902901-chr15:77907031..77910421,4	K562	blood:
5	chr15:77909817..77910574-chr15:77925500..77926398,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1007537	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10459650	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1058129	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2271396	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2271397	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2271398	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs4886519	0.82[ASN][1000 genomes]
rs8027905	0.94[CHB][hapmap]
rs883669	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs907395	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv904419	chr15:77897197-77943935	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2569789	chr15:77910175-77911749	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs907396	STRA6	cis	cerebellum	SCAN
rs907396	ISL2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77901000-77914200	Weak transcription	Right Atrium	heart
2	chr15:77901600-77912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:77903600-77914000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:77904200-77914400	Weak transcription	Brain Substantia Nigra	brain
5	chr15:77904200-77915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:77904600-77914000	Weak transcription	Fetal Lung	lung
7	chr15:77904800-77914200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:77907600-77914400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:77907800-77912600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:77907800-77912600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:77907800-77912800	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:77907800-77914000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:77907800-77914800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:77908000-77910600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:77908000-77914000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:77908000-77914000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:77908000-77914000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:77908000-77914800	Weak transcription	Fetal Intestine Small	intestine
19	chr15:77908000-77918800	Weak transcription	Brain Germinal Matrix	brain
20	chr15:77908200-77914200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:77908400-77914400	Weak transcription	Spleen	Spleen
22	chr15:77908800-77910400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:77909000-77912600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:77909000-77914800	Weak transcription	Fetal Brain Male	brain
25	chr15:77909200-77913800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:77909200-77914200	Weak transcription	Fetal Stomach	stomach
27	chr15:77909400-77910600	Enhancers	Brain Angular Gyrus	brain
28	chr15:77909600-77910600	Enhancers	Fetal Brain Female	brain
29	chr15:77909800-77910400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:77909800-77910400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:77909800-77910400	Enhancers	Pancreas	Pancrea
32	chr15:77909800-77910600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:77909800-77913800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:77909800-77914000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr15:77910000-77910600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:77910000-77910600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:77910000-77910600	Enhancers	K562	blood
38	chr15:77910000-77912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:77910200-77910400	Enhancers	Fetal Heart	heart
40	chr15:77910200-77910600	Flanking Active TSS	HepG2	liver
41	chr15:77910200-77910800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr15:77910200-77914200	Weak transcription	Fetal Muscle Leg	muscle

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