Variant report

Variant	rs10519167
Chromosome Location	chr15:77723027-77723028
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77722169..77724727-chr15:77729292..77731965,2	MCF-7	breast:
2	chr15:77712031..77719483-chr15:77720000..77723368,8	K562	blood:
3	chr15:77709335..77715793-chr15:77716367..77723204,14	MCF-7	breast:
4	chr15:77711837..77714801-chr15:77720000..77724224,8	K562	blood:
5	chr15:77712390..77714805-chr15:77721963..77724729,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10519164	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11629652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11629835	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630843	0.82[ASN][1000 genomes]
rs11631909	0.82[ASN][1000 genomes]
rs11632729	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11634056	0.82[ASN][1000 genomes]
rs11634174	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11636412	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11639293	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11639308	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12898281	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898370	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12898656	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12899552	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12902896	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12903253	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12904254	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12904823	0.81[JPT][hapmap]
rs12909645	0.82[JPT][hapmap]
rs12910951	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12911649	1.00[JPT][hapmap]
rs12911963	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12916682	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12916973	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1554051	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16968835	1.00[CEU][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17383727	0.82[ASN][1000 genomes]
rs17383984	0.82[ASN][1000 genomes]
rs17384406	0.82[ASN][1000 genomes]
rs17385550	0.81[AMR][1000 genomes]
rs17385648	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17469276	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17470228	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2864082	0.82[ASN][1000 genomes]
rs34194537	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34981488	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35235292	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35268067	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35490414	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35902242	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55716459	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62007263	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62008432	0.82[ASN][1000 genomes]
rs7119	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs71407208	0.97[ASN][1000 genomes]
rs7162362	0.81[AMR][1000 genomes]
rs7176254	0.82[ASN][1000 genomes]
rs8032071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040318	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs8040702	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs8042307	0.90[CHB][hapmap];0.92[JPT][hapmap]

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	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10519167	STRA6	cis	cerebellum	SCAN
rs10519167	HMG20A	cis	cerebellum	SCAN
rs10519167	HMG20A	cis	parietal	SCAN
rs10519167	SGK269	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77714000-77726400	Weak transcription	Small Intestine	intestine
2	chr15:77714000-77727600	Weak transcription	Left Ventricle	heart
3	chr15:77714000-77748600	Weak transcription	Placenta	Placenta
4	chr15:77714400-77732400	Weak transcription	HSMM	muscle
5	chr15:77714400-77732800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:77714400-77739200	Weak transcription	Right Atrium	heart
7	chr15:77714400-77741600	Weak transcription	Fetal Thymus	thymus
8	chr15:77714600-77727400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:77714600-77732800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:77714600-77734400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:77714800-77723800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr15:77714800-77739200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:77715000-77740600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:77715400-77733800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:77715400-77737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:77716000-77733800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:77716200-77730200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:77716400-77734200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:77716400-77741400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:77716800-77738000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:77716800-77742600	Weak transcription	Hela-S3	cervix
22	chr15:77717000-77728400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:77717000-77732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:77717000-77754400	Weak transcription	K562	blood
25	chr15:77717200-77739400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:77717800-77725400	Weak transcription	Psoas Muscle	Psoas
27	chr15:77717800-77726400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:77717800-77732600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:77718800-77732000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:77719800-77729000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:77720000-77739400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr15:77720200-77743000	Weak transcription	Primary B cells from cord blood	blood
33	chr15:77720800-77729000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:77721200-77729000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:77721600-77723400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr15:77722000-77723200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:77722000-77723600	Enhancers	GM12878-XiMat	blood
38	chr15:77722600-77723400	Enhancers	Primary T cells from cord blood	blood
39	chr15:77722800-77723200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:77722800-77723200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:77722800-77723200	Enhancers	Right Ventricle	heart
42	chr15:77723000-77723200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:77723000-77728600	Weak transcription	Brain Angular Gyrus	brain

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