Variant report

Variant	rs3850093
Chromosome Location	chr15:75318482-75318483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75318360-75319241	SK-N-MC	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
2	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
3	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
4	chr15:75316003..75319633-chr15:75325409..75329451,5	MCF-7	breast:
5	chr15:75316059..75318846-chr15:75482061..75483763,2	K562	blood:
6	chr15:75300826..75305111-chr15:75313603..75318752,6	MCF-7	breast:
7	chr15:75285958..75287550-chr15:75318167..75319943,2	MCF-7	breast:
8	chr15:75247469..75252493-chr15:75314645..75318771,7	MCF-7	breast:
9	chr15:75316439..75318954-chr15:75442453..75445329,2	K562	blood:
10	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
11	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
12	chr15:75317681..75319554-chr15:75468092..75469844,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000167173	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12185077	0.88[EUR][1000 genomes]
rs12185078	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12185102	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12324912	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12591119	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12591175	0.83[LWK][hapmap]
rs12910644	0.84[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911421	0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12917120	0.82[CHB][hapmap];0.83[YRI][hapmap]
rs13056	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]
rs1867146	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1867150	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120019	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120020	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289582	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2304903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415254	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415255	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34237279	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34713999	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34835684	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35577967	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35736167	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35911108	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3910748	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs5020842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59094290	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60425110	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67324798	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67544533	0.87[EUR][1000 genomes]
rs7166105	0.81[ASW][hapmap];0.85[LWK][hapmap]
rs7173218	0.81[ASW][hapmap];0.89[LWK][hapmap]
rs7175720	0.93[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8028632	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030089	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033837	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8033925	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036573	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8042409	0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8042558	0.87[JPT][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs9672995	0.87[AMR][1000 genomes];0.96[EUR][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
rs3850093	GLCE	cis	cerebellum	SCAN
rs3850093	ULK3	cis	parietal	SCAN
rs3850093	CYP1A1	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75316600-75321000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75316600-75321000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:75316600-75321600	Enhancers	Primary hematopoietic stem cells	blood
4	chr15:75316600-75321800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:75316600-75336800	Weak transcription	Fetal Brain Female	brain
6	chr15:75316800-75318600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:75316800-75318600	Enhancers	Liver	Liver
8	chr15:75316800-75318800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:75316800-75318800	Enhancers	Fetal Thymus	thymus
10	chr15:75316800-75320000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:75316800-75320200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:75316800-75320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75316800-75320600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:75316800-75320800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:75316800-75321000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:75316800-75321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:75316800-75321400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:75316800-75321400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:75316800-75321400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:75316800-75321400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:75316800-75321400	Weak transcription	HUVEC	blood vessel
22	chr15:75316800-75321600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:75316800-75321600	Weak transcription	HMEC	breast
24	chr15:75316800-75321600	Weak transcription	Osteobl	bone
25	chr15:75316800-75321800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:75316800-75321800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:75316800-75321800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:75316800-75321800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:75316800-75321800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:75316800-75321800	Weak transcription	Esophagus	oesophagus
31	chr15:75316800-75321800	Weak transcription	Gastric	stomach
32	chr15:75316800-75321800	Weak transcription	Left Ventricle	heart
33	chr15:75316800-75321800	Weak transcription	Ovary	ovary
34	chr15:75316800-75321800	Weak transcription	Right Atrium	heart
35	chr15:75316800-75321800	Weak transcription	Right Ventricle	heart
36	chr15:75316800-75321800	Weak transcription	Small Intestine	intestine
37	chr15:75316800-75321800	Weak transcription	HSMM	muscle
38	chr15:75316800-75321800	Weak transcription	NH-A	brain
39	chr15:75316800-75321800	Weak transcription	NHDF-Ad	bronchial
40	chr15:75316800-75321800	Weak transcription	NHLF	lung
41	chr15:75316800-75322000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:75316800-75322000	Weak transcription	Brain Angular Gyrus	brain
43	chr15:75316800-75322000	Weak transcription	Fetal Brain Male	brain
44	chr15:75316800-75322000	Weak transcription	Psoas Muscle	Psoas
45	chr15:75316800-75322000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:75316800-75322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:75316800-75322800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:75316800-75338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:75317000-75321800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr15:75317000-75321800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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