Variant report

Variant	rs4775912
Chromosome Location	chr15:51280979-51280980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51280912..51283602-chr15:51286320..51288596,2	MCF-7	breast:
2	chr15:51275705..51277653-chr15:51278587..51281161,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11070815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11633226	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441319	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414092	1.00[CHB][hapmap]
rs2619684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3759808	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803369	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775914	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170736	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[EUR][1000 genomes]
rs72742362	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72744339	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9806270	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4775912	GATM	cis	cerebellum	SCAN
rs4775912	TRPM7	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
2	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:51252400-51283800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:51261600-51295600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:51261600-51298200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:51263000-51304800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:51263400-51281000	Weak transcription	Fetal Heart	heart
8	chr15:51263600-51287200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:51263600-51293600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:51263600-51296400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:51263600-51297800	Weak transcription	NHLF	lung
12	chr15:51263600-51299200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:51263600-51300200	Weak transcription	Small Intestine	intestine
14	chr15:51263600-51301200	Weak transcription	HepG2	liver
15	chr15:51263600-51303000	Weak transcription	HUVEC	blood vessel
16	chr15:51263800-51296200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:51263800-51296600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:51263800-51300400	Weak transcription	Right Ventricle	heart
19	chr15:51264400-51283200	Weak transcription	Brain Substantia Nigra	brain
20	chr15:51264400-51294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:51264600-51296600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:51265200-51292600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:51265200-51296400	Weak transcription	Brain Germinal Matrix	brain
24	chr15:51265200-51302400	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:51265200-51315600	Weak transcription	Gastric	stomach
26	chr15:51265400-51302400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:51266200-51285800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:51266800-51283200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:51266800-51285600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:51267000-51293200	Weak transcription	Fetal Lung	lung
31	chr15:51267000-51302200	Weak transcription	Fetal Brain Female	brain
32	chr15:51267200-51288600	Weak transcription	HMEC	breast
33	chr15:51267200-51289200	Weak transcription	Fetal Kidney	kidney
34	chr15:51267600-51296400	Weak transcription	Fetal Brain Male	brain
35	chr15:51267800-51296400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:51270200-51302600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:51270200-51317600	Weak transcription	Psoas Muscle	Psoas
38	chr15:51271600-51288600	Weak transcription	NHDF-Ad	bronchial
39	chr15:51273000-51296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:51273400-51281800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:51273400-51282600	Weak transcription	Aorta	Aorta
42	chr15:51273400-51285600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:51273400-51285600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:51273400-51285600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:51273400-51288600	Weak transcription	Ovary	ovary
46	chr15:51273400-51296400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:51273400-51296400	Weak transcription	Esophagus	oesophagus
48	chr15:51273400-51298000	Weak transcription	Lung	lung
49	chr15:51273400-51302200	Weak transcription	Colonic Mucosa	Colon
50	chr15:51273400-51302400	Weak transcription	Rectal Smooth Muscle	rectum

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