Variant report

Variant	rs7661412
Chromosome Location	chr4:298772-298773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:297745..300703-chr4:329604..332277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131127	Chromatin interaction
ENSG00000251535	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11727093	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs35476693	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518181	0.83[ASN][1000 genomes]
rs4690243	0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6852858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73791826	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73791827	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
2	nsv1001899	chr4:68809-517736	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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	44 gene(s)	inside rSNPs	diseases
5	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7661412	FLJ90036	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:297400-299400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr4:297400-299600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:297400-300000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:297400-301600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr4:297600-298800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:297600-299400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:297600-299400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:297600-299600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:297600-299600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr4:297600-299600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr4:297600-299600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr4:297600-300600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
13	chr4:297600-301000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:297600-301400	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr4:297800-299400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:297800-299400	ZNF genes & repeats	Spleen	Spleen
17	chr4:297800-299600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:298000-298800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:298000-299200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr4:298000-299400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:298000-299600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:298000-299600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:298000-299600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:298000-299600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:298000-299600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:298000-299600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:298000-299600	Active TSS	Osteobl	bone
28	chr4:298000-299800	Active TSS	Placenta Amnion	Placenta Amnion
29	chr4:298200-298800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:298200-298800	Active TSS	Fetal Intestine Large	intestine
31	chr4:298200-298800	Bivalent/Poised TSS	Fetal Stomach	stomach
32	chr4:298200-299400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:298200-299400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:298200-299400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:298200-299400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:298200-299400	Active TSS	Fetal Heart	heart
37	chr4:298200-299600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:298200-299600	Active TSS	HMEC	breast
39	chr4:298200-299600	Active TSS	HUVEC	blood vessel
40	chr4:298200-299600	Active TSS	NHEK	skin
41	chr4:298400-298800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:298400-298800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr4:298400-298800	Active TSS	Fetal Brain Female	brain
44	chr4:298400-299000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr4:298400-299000	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr4:298400-299000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
47	chr4:298400-299200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:298400-299200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:298400-299200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
50	chr4:298400-299200	Active TSS	Ovary	ovary

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