Variant report

Variant	rs2140175
Chromosome Location	chr15:30213184-30213185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30208802..30211048-chr15:30212481..30214180,2	MCF-7	breast:
2	chr15:30112803..30116771-chr15:30211280..30215308,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11632064	0.88[ASN][1000 genomes]
rs11634609	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12915348	0.84[ASN][1000 genomes]
rs1719343	0.82[EUR][1000 genomes]
rs1719359	0.82[EUR][1000 genomes]
rs1719363	0.84[ASN][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	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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 target site	26 gene(s)	inside rSNPs	diseases
4	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv482572	chr15:30118905-30304529	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv456739	chr15:30178614-30366247	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv568716	chr15:30178614-30366247	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv431371	chr15:30193316-31012794	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2140175	TJP1	cis	cerebellum	SCAN
rs2140175	FAN1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30206800-30216400	Weak transcription	HSMM	muscle
2	chr15:30207200-30213800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:30207200-30216400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:30207200-30216800	Weak transcription	Fetal Kidney	kidney
5	chr15:30209200-30213800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr15:30210000-30213600	Weak transcription	Esophagus	oesophagus
7	chr15:30210800-30213200	Enhancers	Brain Anterior Caudate	brain
8	chr15:30211000-30213800	Enhancers	Brain Hippocampus Middle	brain
9	chr15:30211200-30213800	Enhancers	Brain Angular Gyrus	brain
10	chr15:30211200-30213800	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:30211400-30214400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:30211600-30216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:30211800-30213400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr15:30212000-30213800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:30212000-30214400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:30212000-30214600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:30212200-30213800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:30212200-30213800	Enhancers	NH-A	brain
19	chr15:30212200-30214000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr15:30212200-30214000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:30212400-30213400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:30212400-30214200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:30212600-30213800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr15:30212600-30213800	Enhancers	Fetal Heart	heart
25	chr15:30212600-30213800	Enhancers	Hela-S3	cervix
26	chr15:30212600-30214000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:30212600-30214000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:30212600-30214000	Flanking Active TSS	A549	lung
29	chr15:30212600-30214000	Flanking Active TSS	NHEK	skin
30	chr15:30212600-30214200	Enhancers	Placenta	Placenta
31	chr15:30212800-30213200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:30212800-30213800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:30212800-30213800	Enhancers	Lung	lung
34	chr15:30212800-30213800	Enhancers	Pancreas	Pancrea
35	chr15:30212800-30214000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:30212800-30216600	Weak transcription	Brain Substantia Nigra	brain
37	chr15:30213000-30213200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:30213000-30213200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr15:30213000-30213200	Enhancers	Osteobl	bone
40	chr15:30213000-30213400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:30213000-30213400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr15:30213000-30213600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr15:30213000-30213800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr15:30213000-30213800	Enhancers	Right Ventricle	heart
45	chr15:30213000-30213800	Flanking Active TSS	HMEC	breast
46	chr15:30213000-30214000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr15:30213000-30216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr15:30213000-30216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:30213000-30216800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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