Variant report

Variant	rs2271396
Chromosome Location	chr15:77907535-77907536
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77904241..77907935-chr15:77912354..77915026,5	K562	blood:
2	chr15:77891099..77895017-chr15:77905947..77909078,4	K562	blood:
3	chr15:77901988..77905265-chr15:77907024..77909154,3	MCF-7	breast:
4	chr15:77898597..77902901-chr15:77907031..77910421,4	K562	blood:
5	chr15:77901709..77903452-chr15:77906613..77909214,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10152850	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10459650	0.85[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1058129	0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271397	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2516302	0.87[EUR][1000 genomes]
rs2667764	0.87[EUR][1000 genomes]
rs2667767	0.84[EUR][1000 genomes]
rs2682910	0.87[EUR][1000 genomes]
rs2867311	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2867312	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886519	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886883	0.89[EUR][1000 genomes]
rs4886889	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57471224	0.89[EUR][1000 genomes]
rs59745219	0.89[EUR][1000 genomes]
rs60701760	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7497168	0.87[EUR][1000 genomes]
rs8027905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867916	0.88[EUR][1000 genomes]
rs883669	0.89[CEU][hapmap]
rs907374	0.90[EUR][1000 genomes]
rs907390	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907392	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907393	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907395	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs907396	0.85[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs938090	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2271396	STRA6	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77899800-77908000	Weak transcription	Ovary	ovary
2	chr15:77901000-77914200	Weak transcription	Right Atrium	heart
3	chr15:77901600-77912800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:77903600-77914000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:77904200-77914400	Weak transcription	Brain Substantia Nigra	brain
6	chr15:77904200-77915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:77904600-77909000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:77904600-77910000	Weak transcription	K562	blood
9	chr15:77904600-77914000	Weak transcription	Fetal Lung	lung
10	chr15:77904800-77907600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:77904800-77908000	Strong transcription	Brain Germinal Matrix	brain
12	chr15:77904800-77909600	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:77904800-77914200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:77905000-77909000	Strong transcription	Fetal Brain Female	brain
15	chr15:77905200-77907800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:77905200-77908000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:77905400-77908000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:77905400-77909200	Strong transcription	Fetal Stomach	stomach
19	chr15:77905600-77909400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:77905800-77908000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:77906000-77908200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr15:77906200-77907800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr15:77906200-77908000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:77906200-77908000	Strong transcription	Fetal Intestine Small	intestine
25	chr15:77906400-77907600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77906400-77907600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
27	chr15:77906400-77907800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr15:77906400-77907800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:77906400-77907800	Strong transcription	Pancreas	Pancrea
30	chr15:77906400-77907800	ZNF genes & repeats	Spleen	Spleen
31	chr15:77906400-77908000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:77906600-77907600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:77906600-77907800	Strong transcription	Brain Cingulate Gyrus	brain
34	chr15:77906600-77907800	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:77906600-77908000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:77906600-77908200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:77906800-77908000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:77907000-77907800	Strong transcription	Brain Angular Gyrus	brain
39	chr15:77907200-77907600	Strong transcription	Brain Anterior Caudate	brain
40	chr15:77907200-77907800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links