Variant report

Variant	rs12903781
Chromosome Location	chr15:52067655-52067656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51960322..51962005-chr15:52066189..52068560,2	MCF-7	breast:
2	chr15:52041578..52043683-chr15:52065420..52068365,2	K562	blood:
3	chr15:52066782..52068906-chr15:52166173..52168247,2	K562	blood:
4	chr15:52028686..52030941-chr15:52066713..52069021,2	MCF-7	breast:
5	chr15:51934747..51936336-chr15:52066593..52068125,2	MCF-7	breast:
6	chr15:51942270..51945778-chr15:52064444..52070724,6	MCF-7	breast:
7	chr15:51938680..51944458-chr15:52065543..52071230,9	K562	blood:
8	chr15:51941829..51942488-chr15:52067554..52068054,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1035737	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs10851503	0.87[ASN][1000 genomes]
rs10851504	0.87[ASN][1000 genomes]
rs11049	0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11630253	0.81[ASN][1000 genomes]
rs11630579	0.83[CHB][hapmap]
rs12591672	0.81[ASN][1000 genomes]
rs12592771	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12593708	0.89[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs12901638	0.84[ASN][1000 genomes]
rs12902930	0.89[ASN][1000 genomes]
rs12908327	0.94[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12913850	0.86[ASN][1000 genomes]
rs12915015	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12915568	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs17526760	0.94[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs17539905	0.81[ASN][1000 genomes]
rs17705817	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[ASN][1000 genomes]
rs2007335	0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2007355	0.94[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2010026	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2011995	0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2052708	0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2114191	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2414122	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2433217	0.88[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2433221	0.89[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs2436655	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2436656	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs2436660	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2441780	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2448946	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2448947	0.84[ASN][1000 genomes]
rs2448948	0.81[ASN][1000 genomes]
rs2448950	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2448953	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2470599	0.84[ASN][1000 genomes]
rs2470600	0.81[ASN][1000 genomes]
rs2470601	0.84[ASN][1000 genomes]
rs2470608	0.81[ASN][1000 genomes]
rs2470610	0.83[ASN][1000 genomes]
rs2470611	0.81[ASN][1000 genomes]
rs2470612	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2470615	1.00[ASW][hapmap];0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs2470618	0.84[ASN][1000 genomes]
rs2912186	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2912187	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2912188	0.81[ASN][1000 genomes]
rs2912189	0.94[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2916169	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2916170	0.84[ASN][1000 genomes]
rs2916171	0.84[ASN][1000 genomes]
rs2916172	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916175	0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916176	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916177	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2921951	0.84[ASN][1000 genomes]
rs2921953	0.83[ASN][1000 genomes]
rs2929423	0.89[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2929424	0.88[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2929425	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2929428	0.83[ASN][1000 genomes]
rs2959285	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2959291	0.80[ASN][1000 genomes]
rs2959293	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2959298	0.94[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2959299	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2959300	0.83[ASN][1000 genomes]
rs2959305	0.84[ASN][1000 genomes]
rs2959306	0.81[ASN][1000 genomes]
rs2959307	0.83[ASN][1000 genomes]
rs36087956	0.84[ASN][1000 genomes]
rs62016192	0.81[ASN][1000 genomes]
rs6493525	0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6493526	0.94[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7162925	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs7163541	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7170910	0.91[ASN][1000 genomes]
rs72732914	0.84[ASN][1000 genomes]
rs8028486	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8033433	0.91[ASN][1000 genomes]
rs8035126	0.88[ASN][1000 genomes]
rs8038344	0.89[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12903781	SCG3	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
4	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
5	chr15:52052200-52068600	Weak transcription	HMEC	breast
6	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
8	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
9	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
10	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
11	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:52052600-52106600	Weak transcription	HSMM	muscle
13	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
14	chr15:52058600-52068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:52060200-52068200	Weak transcription	Liver	Liver
17	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:52060400-52068400	Strong transcription	Thymus	Thymus
19	chr15:52060400-52069200	Weak transcription	Placenta	Placenta
20	chr15:52060400-52069800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr15:52060400-52079200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
23	chr15:52060600-52068600	Weak transcription	Brain Substantia Nigra	brain
24	chr15:52060600-52069000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:52060600-52073400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:52060600-52073600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:52060600-52087400	Weak transcription	Gastric	stomach
28	chr15:52060600-52088400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
30	chr15:52060800-52067800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:52060800-52068400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:52060800-52068600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr15:52060800-52074600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:52060800-52101200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:52060800-52102600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:52060800-52105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:52061000-52068400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:52061000-52069800	Strong transcription	Primary T cells from cord blood	blood
39	chr15:52061000-52074400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr15:52061600-52073600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:52061600-52085400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:52061600-52112000	Weak transcription	NHLF	lung
43	chr15:52061800-52073600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:52061800-52076200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:52061800-52077200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:52061800-52098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:52062800-52068600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:52063000-52073000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:52063000-52074600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:52063800-52068200	Weak transcription	K562	blood

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