Variant report

Variant	rs17556255
Chromosome Location	chr18:7748979-7748980
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	chr18:7745866..7749831-chr18:7752461..7755443,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173482	Chromatin interaction
ENSG00000266767	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10853357	0.85[EUR][1000 genomes]
rs11660897	0.86[EUR][1000 genomes]
rs12605941	0.85[EUR][1000 genomes]
rs1446077	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446078	0.85[EUR][1000 genomes]
rs1446085	0.85[EUR][1000 genomes]
rs17556324	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1940345	0.85[EUR][1000 genomes]
rs2027670	0.85[EUR][1000 genomes]
rs4455047	0.85[EUR][1000 genomes]
rs4798582	0.85[EUR][1000 genomes]
rs4798584	0.85[EUR][1000 genomes]
rs4798585	0.85[EUR][1000 genomes]
rs4798587	0.83[EUR][1000 genomes]
rs4798591	0.85[EUR][1000 genomes]
rs4798592	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9964890	0.85[EUR][1000 genomes]
rs9973158	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1064869	chr18:7730116-7760969	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1061538	chr18:7730116-7762149	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1067394	chr18:7730116-7768536	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2656311	chr18:7732141-7761056	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1057760	chr18:7732188-7760969	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv431970	chr18:7732188-7770950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv525328	chr18:7732917-7760498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv576421	chr18:7732917-7761056	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv576422	chr18:7732917-7763363	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv576423	chr18:7732917-7788329	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv576424	chr18:7740473-7761056	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7739000-7750600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:7742000-7751400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr18:7744200-7749000	Weak transcription	Brain Anterior Caudate	brain
4	chr18:7745600-7750800	Weak transcription	Aorta	Aorta
5	chr18:7746600-7750000	Enhancers	Left Ventricle	heart
6	chr18:7746600-7750000	Enhancers	Psoas Muscle	Psoas
7	chr18:7746600-7750000	Enhancers	Right Atrium	heart
8	chr18:7746800-7749800	Enhancers	Lung	lung
9	chr18:7746800-7749800	Enhancers	Spleen	Spleen
10	chr18:7746800-7751400	Enhancers	Right Ventricle	heart
11	chr18:7746800-7752000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr18:7746800-7753600	Enhancers	HepG2	liver
13	chr18:7747000-7752000	Enhancers	Fetal Heart	heart
14	chr18:7747200-7750200	Enhancers	Colon Smooth Muscle	Colon
15	chr18:7747400-7749000	Weak transcription	Fetal Intestine Large	intestine
16	chr18:7747600-7749000	Weak transcription	Fetal Intestine Small	intestine
17	chr18:7747600-7750000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr18:7748000-7749200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr18:7748000-7749400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:7748000-7749400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr18:7748000-7749800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr18:7748000-7750000	Flanking Active TSS	Fetal Thymus	thymus
23	chr18:7748000-7750400	Enhancers	Rectal Smooth Muscle	rectum
24	chr18:7748000-7751000	Enhancers	HUVEC	blood vessel
25	chr18:7748200-7749200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr18:7748200-7749400	Weak transcription	Small Intestine	intestine
27	chr18:7748200-7749800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:7748200-7749800	Enhancers	Brain Substantia Nigra	brain
29	chr18:7748200-7749800	Enhancers	Ovary	ovary
30	chr18:7748200-7749800	Enhancers	Pancreas	Pancrea
31	chr18:7748200-7750000	Enhancers	Primary hematopoietic stem cells	blood
32	chr18:7748200-7750000	Enhancers	Placenta	Placenta
33	chr18:7748200-7750000	Enhancers	Osteobl	bone
34	chr18:7748200-7750600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr18:7748200-7750800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr18:7748200-7751400	Enhancers	Fetal Kidney	kidney
37	chr18:7748400-7749600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:7748400-7749800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:7748400-7749800	Enhancers	Brain Cingulate Gyrus	brain
40	chr18:7748400-7749800	Enhancers	Fetal Lung	lung
41	chr18:7748400-7750000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:7748400-7750000	Enhancers	Fetal Stomach	stomach
43	chr18:7748400-7750200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr18:7748400-7750200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr18:7748400-7750800	Enhancers	Fetal Muscle Leg	muscle
46	chr18:7748400-7751800	Enhancers	A549	lung
47	chr18:7748600-7749000	Weak transcription	Gastric	stomach
48	chr18:7748600-7749000	Active TSS	Thymus	Thymus
49	chr18:7748600-7750000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:7748600-7751400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links