Variant report

Variant	rs13056
Chromosome Location	chr15:75312187-75312188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75289096..75291038-chr15:75311135..75313518,2	K562	blood:
2	chr15:75197976..75200333-chr15:75311534..75313971,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs12148488	0.85[YRI][hapmap]
rs12185077	0.86[EUR][1000 genomes]
rs12185078	0.83[AMR][1000 genomes]
rs12185102	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12324912	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591119	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12593542	0.85[LWK][hapmap]
rs12593566	0.82[YRI][hapmap]
rs12898259	0.82[AFR][1000 genomes]
rs12900654	0.82[YRI][hapmap]
rs12901243	0.82[AFR][1000 genomes]
rs12903201	0.82[AFR][1000 genomes]
rs12910644	0.84[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12911421	0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12917120	0.89[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1867146	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867150	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2083730	0.82[YRI][hapmap]
rs2083731	0.82[AFR][1000 genomes]
rs2120019	1.00[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120020	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289582	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2304899	0.92[YRI][hapmap]
rs2304903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2415253	0.82[AFR][1000 genomes]
rs2415254	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2415255	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34237279	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34655806	0.82[AFR][1000 genomes]
rs34713999	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34835684	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35577967	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35736167	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35911108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812944	0.92[YRI][hapmap]
rs3850093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3910748	0.81[LWK][hapmap]
rs4886651	0.82[YRI][hapmap]
rs5020842	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59094290	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60425110	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61166993	0.81[AFR][1000 genomes]
rs6495135	0.83[ASW][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap]
rs6495138	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs6495140	0.81[AFR][1000 genomes]
rs6495143	0.82[YRI][hapmap]
rs6495147	0.81[AFR][1000 genomes]
rs67324798	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67544533	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7162900	0.81[AFR][1000 genomes]
rs7163390	0.89[LWK][hapmap]
rs7163636	0.92[YRI][hapmap]
rs7167415	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs7168680	0.81[AFR][1000 genomes]
rs7173218	0.81[LWK][hapmap]
rs7173833	0.82[AFR][1000 genomes]
rs7174129	0.83[ASW][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs7175720	0.92[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181942	0.81[AFR][1000 genomes]
rs7342591	0.82[ASW][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs7342601	0.83[ASW][hapmap];0.89[LWK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs8028632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030089	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031545	0.82[YRI][hapmap]
rs8033837	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8033925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036197	0.82[AFR][1000 genomes]
rs8036573	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8039755	0.92[YRI][hapmap]
rs8040169	0.82[AFR][1000 genomes]
rs8042409	0.92[CEU][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042558	0.83[ASW][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap]
rs9672995	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9673012	0.81[YRI][hapmap]
rs9788648	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13056	GLCE	cis	cerebellum	SCAN
rs13056	ULK3	cis	parietal	SCAN
rs13056	CYP1A1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
3	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
4	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
6	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
8	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
9	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
10	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
15	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
18	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:75304800-75312600	Strong transcription	Brain Anterior Caudate	brain
20	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
22	chr15:75306000-75312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
24	chr15:75307800-75315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:75308200-75315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:75308600-75313800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:75308800-75312800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr15:75309000-75312600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:75309000-75315800	Weak transcription	Placenta	Placenta
30	chr15:75309400-75312600	Strong transcription	Gastric	stomach
31	chr15:75309400-75315600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:75309800-75313600	Strong transcription	Brain Hippocampus Middle	brain
33	chr15:75310000-75313600	Strong transcription	Brain Cingulate Gyrus	brain
34	chr15:75310000-75313600	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr15:75310000-75315200	Weak transcription	Brain Substantia Nigra	brain
36	chr15:75310200-75315200	Weak transcription	HepG2	liver
37	chr15:75310400-75315800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:75310800-75312800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr15:75310800-75313600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:75310800-75314000	Strong transcription	Brain Germinal Matrix	brain
41	chr15:75311000-75312200	Weak transcription	Pancreas	Pancrea
42	chr15:75311000-75315600	Weak transcription	Liver	Liver
43	chr15:75311000-75315600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:75311200-75315800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:75311200-75315800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:75311400-75312400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:75311400-75312800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:75311400-75313200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:75311400-75315400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:75311400-75315800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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