Variant report

Variant	rs12535455
Chromosome Location	chr7:97877518-97877519
allele	C/G
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	CTCF	chr7:97877460-97877610	Caco-2	colon:	n/a	chr7:97877555-97877564

Variant related genes	Relation type
TECPR1	TF binding region
BRI3	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11983144	0.87[ASN][1000 genomes]
rs13231773	0.87[ASN][1000 genomes]
rs2270595	0.93[ASN][1000 genomes]
rs4727389	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729420	0.90[AMR][1000 genomes]
rs61255730	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66486729	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7791314	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS 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 miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97841200-97880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:97841400-97879400	Weak transcription	Fetal Brain Male	brain
3	chr7:97841400-97880200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:97848000-97877600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:97848000-97880600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:97850000-97878000	Strong transcription	Fetal Stomach	stomach
7	chr7:97850400-97878600	Weak transcription	GM12878-XiMat	blood
8	chr7:97852000-97878000	Weak transcription	Small Intestine	intestine
9	chr7:97853200-97880000	Weak transcription	A549	lung
10	chr7:97853400-97880200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:97857000-97879000	Strong transcription	Brain Germinal Matrix	brain
12	chr7:97858200-97878200	Weak transcription	Stomach Mucosa	stomach
13	chr7:97858200-97879000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:97859200-97880200	Weak transcription	Psoas Muscle	Psoas
15	chr7:97859800-97878200	Weak transcription	HepG2	liver
16	chr7:97860200-97878400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:97862000-97877800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:97864600-97880200	Weak transcription	NHDF-Ad	bronchial
19	chr7:97864600-97880200	Weak transcription	NHEK	skin
20	chr7:97865000-97878600	Strong transcription	Fetal Intestine Small	intestine
21	chr7:97865200-97880200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:97865400-97878600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:97866000-97880400	Weak transcription	Fetal Kidney	kidney
24	chr7:97867200-97877600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr7:97867600-97877600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr7:97868200-97880200	Weak transcription	HSMM	muscle
27	chr7:97868600-97880000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr7:97868800-97880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:97868800-97880200	Weak transcription	Colon Smooth Muscle	Colon
30	chr7:97869000-97880600	Weak transcription	NH-A	brain
31	chr7:97869800-97878400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:97870400-97880000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:97870400-97880000	Weak transcription	Hela-S3	cervix
34	chr7:97870600-97877800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr7:97870800-97880200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:97871200-97880000	Weak transcription	Fetal Lung	lung
37	chr7:97871400-97880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:97871600-97879600	Weak transcription	Fetal Intestine Large	intestine
39	chr7:97871600-97880200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:97871800-97878000	Weak transcription	Primary B cells from cord blood	blood
41	chr7:97871800-97880400	Weak transcription	Osteobl	bone
42	chr7:97872800-97878800	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr7:97873800-97880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr7:97874000-97878200	Weak transcription	Fetal Thymus	thymus
45	chr7:97874000-97878400	Weak transcription	Dnd41	blood
46	chr7:97874000-97879800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:97874000-97880000	Weak transcription	Brain Angular Gyrus	brain
48	chr7:97874000-97880000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:97874000-97880200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:97874000-97880200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links