Variant report

Variant	rs7764616
Chromosome Location	chr6:45545975-45545976
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	TCF12	chr6:45545477-45546028	SK-N-SH	brain:	n/a	n/a
2	EP300	chr6:45545602-45546072	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr6:45545643-45546112	SK-N-SH_RA	brain:	n/a	n/a
4	MEF2A	chr6:45545510-45546099	SK-N-SH	brain:	n/a	chr6:45545804-45545818 chr6:45545803-45545819 chr6:45545804-45545820 chr6:45545800-45545821 chr6:45545807-45545816 chr6:45545802-45545823 chr6:45545802-45545823 chr6:45545804-45545819 chr6:45545802-45545823 chr6:45545806-45545817

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45538385..45540491-chr6:45545062..45546957,2	MCF-7	breast:
2	chr6:45545471..45547955-chr6:45549621..45552271,2	K562	blood:

Variant related genes	Relation type
ENSG00000261080	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10485421	0.91[ASN][1000 genomes]
rs10948241	0.90[ASN][1000 genomes]
rs11753640	0.91[ASN][1000 genomes]
rs35454036	0.91[ASN][1000 genomes]
rs4711819	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711820	0.91[ASN][1000 genomes]
rs4711821	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740614	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7754569	0.91[ASN][1000 genomes]
rs9296461	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv462940	chr6:45532214-45545975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv603010	chr6:45532214-45545975	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7764616	YIPF3	cis	parietal	SCAN
rs7764616	C6orf138	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45537400-45559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:45537600-45546000	Weak transcription	Right Atrium	heart
3	chr6:45542800-45554000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:45544600-45546200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:45544600-45546400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:45544800-45546000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:45544800-45546000	Enhancers	Brain Germinal Matrix	brain
8	chr6:45544800-45546200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:45544800-45546200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:45544800-45546200	Enhancers	Fetal Stomach	stomach
11	chr6:45544800-45546200	Enhancers	HSMM	muscle
12	chr6:45544800-45546200	Enhancers	HSMMtube	muscle
13	chr6:45544800-45546200	Enhancers	NHLF	lung
14	chr6:45544800-45546600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:45544800-45546600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:45545000-45546000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:45545000-45546000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:45545000-45546000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:45545000-45546000	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:45545000-45546000	Weak transcription	Placenta	Placenta
21	chr6:45545000-45546000	Weak transcription	Left Ventricle	heart
22	chr6:45545000-45546000	Weak transcription	Right Ventricle	heart
23	chr6:45545000-45546200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:45545000-45546200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:45545000-45546200	Enhancers	Osteobl	bone
26	chr6:45545200-45546000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:45545200-45546200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:45545200-45546200	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:45545200-45546200	Enhancers	Brain Substantia Nigra	brain
30	chr6:45545200-45546400	Enhancers	Fetal Lung	lung
31	chr6:45545200-45546400	Enhancers	NH-A	brain
32	chr6:45545400-45546200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:45545400-45546600	Enhancers	HUVEC	blood vessel
34	chr6:45545600-45546200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:45545600-45546200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:45545600-45546200	Enhancers	Brain Hippocampus Middle	brain
37	chr6:45545600-45546400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:45545800-45546000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:45545800-45546400	Enhancers	Lung	lung
40	chr6:45545800-45546400	Enhancers	Ovary	ovary
41	chr6:45545800-45546400	Enhancers	NHDF-Ad	bronchial

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