Variant report

Variant	rs4555110
Chromosome Location	chr15:74671525-74671526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74670584..74672093-chr15:74907235..74909919,2	MCF-7	breast:
2	chr15:74667595..74674345-chr15:74676249..74682092,7	K562	blood:
3	chr15:74670802..74672739-chr15:74752255..74754847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138629	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000247240	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11072479	0.84[AFR][1000 genomes]
rs12438594	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12913682	0.81[AFR][1000 genomes]
rs16968477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2073475	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279357	0.84[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs28681535	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825944	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3935523	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4077583	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4077584	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4077585	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4505257	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4598865	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58844886	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60636222	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7167038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180256	1.00[YRI][hapmap]
rs7180275	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7181947	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9944175	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4555110	NRG4	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74666600-74673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:74667200-74676400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:74667400-74673600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:74667400-74676800	Weak transcription	Colonic Mucosa	Colon
5	chr15:74667400-74691200	Enhancers	Placenta	Placenta
6	chr15:74667600-74671600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:74667600-74673800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:74667600-74674000	Weak transcription	NHDF-Ad	bronchial
9	chr15:74667600-74674600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:74667600-74675600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr15:74667600-74675800	Weak transcription	A549	lung
12	chr15:74667600-74676000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:74667600-74677600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:74667600-74677600	Weak transcription	Right Atrium	heart
15	chr15:74667800-74674600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:74667800-74675000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:74667800-74676000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:74668000-74675000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:74668400-74672200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:74669400-74671800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:74669400-74671800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:74670600-74671800	Enhancers	Primary T cells from cord blood	blood
23	chr15:74670600-74671800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:74670600-74671800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:74670600-74671800	Enhancers	HSMMtube	muscle
26	chr15:74670600-74671800	Enhancers	NHEK	skin
27	chr15:74670600-74672000	Enhancers	Primary hematopoietic stem cells	blood
28	chr15:74670600-74672000	Enhancers	HMEC	breast
29	chr15:74670800-74671800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr15:74670800-74678600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:74671000-74671800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:74671000-74671800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:74671000-74671800	Enhancers	Fetal Thymus	thymus
34	chr15:74671000-74671800	Enhancers	NH-A	brain
35	chr15:74671000-74672000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr15:74671000-74672000	Enhancers	Fetal Kidney	kidney
37	chr15:74671200-74671600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:74671200-74671600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr15:74671200-74671600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:74671200-74671600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:74671200-74671600	Enhancers	Esophagus	oesophagus
42	chr15:74671200-74671800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:74671200-74671800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr15:74671200-74671800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr15:74671200-74671800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr15:74671200-74671800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:74671200-74671800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:74671200-74671800	Enhancers	Primary B cells from peripheral blood	blood
49	chr15:74671200-74671800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr15:74671200-74671800	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links