Variant report

Variant	rs11931598
Chromosome Location	chr4:7047102-7047103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr4:7047027-7047171	H1-hESC	embryonic stem cell:	n/a	n/a
2	WRNIP1	chr4:7046796-7047174	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7041999..7051916-chr4:7066728..7075643,37	MCF-7	breast:
2	chr4:7042421..7051559-chr4:7062214..7072674,24	MCF-7	breast:

Variant related genes	Relation type
CCDC96	TF binding region
ENSG00000109519	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10937780	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs28385900	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28661210	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4689581	0.96[ASN][1000 genomes]
rs870660	0.82[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv878533	chr4:7032180-7063524	Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv4217	chr4:7035512-7080230	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1801315	chr4:7044007-7052777	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1835149	chr4:7044007-7052777	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv593556	chr4:7044447-7048842	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv1798014	chr4:7044504-7052182	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11931598	GRPEL1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7045400-7048000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr4:7045600-7047200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:7045600-7047200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr4:7045600-7047200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr4:7045800-7047200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr4:7045800-7047200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr4:7045800-7047200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:7045800-7047400	Flanking Active TSS	Fetal Lung	lung
9	chr4:7045800-7047600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:7045800-7047600	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr4:7045800-7048200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr4:7045800-7049400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:7046000-7047400	Flanking Active TSS	Fetal Brain Female	brain
14	chr4:7046000-7047600	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr4:7046200-7047200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:7046200-7047200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:7046200-7047200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:7046200-7047200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr4:7046200-7047200	Flanking Active TSS	Fetal Heart	heart
20	chr4:7046200-7047200	Flanking Active TSS	Hela-S3	cervix
21	chr4:7046200-7047400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr4:7046200-7047600	Flanking Active TSS	Pancreas	Pancrea
23	chr4:7046200-7047800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr4:7046200-7048000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr4:7046200-7048800	Flanking Active TSS	HSMM	muscle
26	chr4:7046200-7068600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:7046400-7047200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr4:7046400-7047200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr4:7046400-7047200	Enhancers	Placenta	Placenta
30	chr4:7046400-7047400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:7046400-7047400	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr4:7046400-7047600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:7046400-7047800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr4:7046400-7048000	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr4:7046400-7048000	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr4:7046400-7049000	Flanking Active TSS	GM12878-XiMat	blood
37	chr4:7046400-7049800	Enhancers	Primary B cells from peripheral blood	blood
38	chr4:7046400-7049800	Genic enhancers	Spleen	Spleen
39	chr4:7046600-7047200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:7046600-7047200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:7046600-7047200	Enhancers	Aorta	Aorta
42	chr4:7046600-7047800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:7046600-7047800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:7046600-7047800	Enhancers	Thymus	Thymus
45	chr4:7046600-7047800	Enhancers	K562	blood
46	chr4:7046600-7048000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr4:7046600-7048400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:7046600-7048600	Enhancers	Small Intestine	intestine
49	chr4:7046600-7049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:7046600-7050400	Enhancers	Lung	lung

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