Variant report

Variant	rs12593327
Chromosome Location	chr15:75954096-75954097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75951981..75955869-chr15:75961912..75967583,8	MCF-7	breast:
2	chr15:75930676..75935484-chr15:75948921..75956484,11	MCF-7	breast:
3	chr15:75952724..75954958-chr15:75955903..75959191,3	K562	blood:
4	chr15:75952729..75955178-chr15:75965202..75967064,2	K562	blood:
5	chr15:75953724..75957700-chr15:75974147..75976350,4	MCF-7	breast:
6	chr15:75953678..75955508-chr15:75964203..75966702,2	K562	blood:
7	chr15:75953121..75955415-chr15:76012310..76015183,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177971	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11072554	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11632887	0.95[LWK][hapmap];0.81[YRI][hapmap]
rs4243036	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886727	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7164179	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
4	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
7	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527186	chr15:75924443-76107730	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
9	nsv904391	chr15:75930757-76001654	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv904392	chr15:75930757-76039262	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
11	nsv904393	chr15:75932177-76001654	Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv984485	chr15:75932760-75965433	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv904394	chr15:75948671-76039262	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12593327	NRG4	cis	cerebellum	SCAN
rs12593327	MAN2C1	cis	parietal	SCAN
rs12593327	NRG4	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75944600-75954400	Genic enhancers	Lung	lung
2	chr15:75945000-75954400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:75945200-75955000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:75946800-75956600	Weak transcription	K562	blood
5	chr15:75947200-75955200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:75948800-75954200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:75948800-75957400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:75950400-75964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:75950600-75957200	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr15:75950600-75959200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:75950800-75956200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:75950800-75957600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr15:75951000-75954400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr15:75951200-75954200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:75951400-75954600	Weak transcription	Brain Germinal Matrix	brain
16	chr15:75951400-75955400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:75951400-75956600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:75951600-75956000	Enhancers	NHDF-Ad	bronchial
19	chr15:75952000-75954400	Enhancers	Brain Substantia Nigra	brain
20	chr15:75952000-75954400	Enhancers	Right Atrium	heart
21	chr15:75952400-75954600	Enhancers	NH-A	brain
22	chr15:75952600-75954200	Genic enhancers	A549	lung
23	chr15:75952600-75954400	Genic enhancers	Fetal Stomach	stomach
24	chr15:75952600-75954600	Enhancers	Liver	Liver
25	chr15:75952800-75954400	Genic enhancers	Fetal Intestine Small	intestine
26	chr15:75952800-75956600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:75953000-75954200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:75953000-75954200	Enhancers	Fetal Thymus	thymus
29	chr15:75953000-75954200	Enhancers	Left Ventricle	heart
30	chr15:75953000-75954200	Enhancers	Spleen	Spleen
31	chr15:75953000-75954200	Enhancers	HUVEC	blood vessel
32	chr15:75953000-75954400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:75953000-75954400	Enhancers	Placenta	Placenta
34	chr15:75953000-75954400	Enhancers	Ovary	ovary
35	chr15:75953000-75954400	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr15:75953000-75954400	Flanking Active TSS	Hela-S3	cervix
37	chr15:75953000-75954600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:75953000-75956000	Enhancers	Esophagus	oesophagus
39	chr15:75953000-75957400	Enhancers	Duodenum Mucosa	Duodenum
40	chr15:75953000-75969600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:75953200-75954200	Enhancers	Fetal Intestine Large	intestine
42	chr15:75953200-75954200	Flanking Active TSS	HSMM	muscle
43	chr15:75953200-75954400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:75953200-75954400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:75953200-75955000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:75953200-75955200	Enhancers	Fetal Muscle Leg	muscle
47	chr15:75953200-75955600	Weak transcription	Fetal Kidney	kidney
48	chr15:75953200-75955600	Enhancers	HMEC	breast
49	chr15:75953200-75957200	Enhancers	Pancreas	Pancrea
50	chr15:75953200-75958400	Weak transcription	Right Ventricle	heart

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