Variant report

Variant	rs327078
Chromosome Location	chr4:187595058-187595059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187594872..187597039-chr4:187644537..187647296,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs162063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162182	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192997	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28532777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327111	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3733409	0.80[CHB][hapmap]
rs456000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs462509	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1015619	chr4:187442453-187595058	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv881509	chr4:187574398-187614434	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs327078	FAM149A	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187573000-187605400	Weak transcription	Gastric	stomach
2	chr4:187573200-187596600	Weak transcription	Esophagus	oesophagus
3	chr4:187579600-187595400	Weak transcription	Brain Substantia Nigra	brain
4	chr4:187583000-187614400	Weak transcription	Colonic Mucosa	Colon
5	chr4:187587600-187610200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:187587800-187597000	Weak transcription	Fetal Kidney	kidney
7	chr4:187588400-187597800	Weak transcription	Stomach Mucosa	stomach
8	chr4:187588400-187604400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:187590600-187595600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:187590600-187596800	Weak transcription	Right Ventricle	heart
11	chr4:187591200-187595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:187591200-187597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:187591200-187597200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:187591200-187598000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:187591200-187604000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:187591200-187607000	Weak transcription	Adipose Nuclei	Adipose
17	chr4:187591200-187614400	Weak transcription	Ovary	ovary
18	chr4:187591400-187595400	Weak transcription	Fetal Intestine Small	intestine
19	chr4:187591400-187596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:187591400-187596400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:187591400-187596800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:187591400-187597000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:187591400-187597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:187591400-187597600	Weak transcription	Fetal Lung	lung
25	chr4:187591400-187597800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:187591400-187597800	Weak transcription	Fetal Stomach	stomach
27	chr4:187591400-187603800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:187591400-187604400	Weak transcription	Fetal Muscle Leg	muscle
29	chr4:187591600-187596600	Weak transcription	HSMMtube	muscle
30	chr4:187591600-187596800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:187591600-187597000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:187591600-187597600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:187591800-187597000	Weak transcription	NH-A	brain
34	chr4:187591800-187597000	Weak transcription	Osteobl	bone
35	chr4:187592000-187597800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:187592200-187596200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:187592200-187596800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:187592200-187598000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:187592200-187604000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:187592200-187605400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:187592400-187596200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:187592400-187597600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:187592600-187597200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:187593000-187595800	Enhancers	Fetal Heart	heart
45	chr4:187593200-187597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:187593200-187597800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:187593400-187595600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:187593400-187596000	Strong transcription	HMEC	breast
49	chr4:187593400-187596800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:187593800-187596600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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