Variant report

Variant	rs7794089
Chromosome Location	chr7:101245304-101245305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101242393..101247738-chr7:101456834..101460384,5	MCF-7	breast:
2	chr7:101245091..101246357-chr7:101457101..101458459,9	MCF-7	breast:
3	chr7:101244039..101255564-chr7:101454524..101463981,21	MCF-7	breast:
4	chr7:101239160..101242958-chr7:101243756..101248056,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs62466270	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62466272	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7778019	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv888821	chr7:101091470-101311540	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv831078	chr7:101094945-101257486	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv888822	chr7:101105017-101330734	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv888824	chr7:101109073-101330734	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888825	chr7:101168283-101330734	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv888826	chr7:101230768-101277334	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7794089	MCM7	cis	parietal	SCAN
rs7794089	FAM185A	cis	cerebellum	SCAN
rs7794089	CUX1	cis	cerebellum	SCAN
rs7794089	DPY19L2P2	cis	parietal	SCAN
rs7794089	RPL35	trans	cerebellum	SCAN
rs7794089	COPS6	cis	parietal	SCAN
rs7794089	FIS1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101241400-101246200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:101242200-101245600	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:101242200-101249600	Weak transcription	Spleen	Spleen
4	chr7:101242400-101245400	Weak transcription	HSMM	muscle
5	chr7:101242400-101245800	Weak transcription	HMEC	breast
6	chr7:101242400-101246200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:101242400-101248400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:101242600-101245400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:101242600-101245600	Weak transcription	Fetal Intestine Small	intestine
10	chr7:101242600-101245800	Weak transcription	Colonic Mucosa	Colon
11	chr7:101242600-101245800	Weak transcription	Pancreas	Pancrea
12	chr7:101242600-101248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:101242600-101248800	Weak transcription	Fetal Lung	lung
14	chr7:101242800-101245400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:101242800-101245600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:101242800-101246000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:101242800-101246000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:101242800-101251600	Weak transcription	Gastric	stomach
19	chr7:101243000-101245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:101243000-101246000	Weak transcription	HSMMtube	muscle
21	chr7:101243200-101245400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:101243200-101246000	Weak transcription	NHDF-Ad	bronchial
23	chr7:101243600-101245600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr7:101245000-101245400	Bivalent Enhancer	HepG2	liver
25	chr7:101245000-101246400	Enhancers	Fetal Intestine Large	intestine
26	chr7:101245200-101245600	Bivalent Enhancer	Placenta	Placenta
27	chr7:101245200-101246600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
28	chr7:101245200-101246800	Enhancers	Fetal Muscle Leg	muscle

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