Variant report

Variant	rs17743799
Chromosome Location	chr18:29963113-29963114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29962611..29966946-chr18:30048395..30051891,4	MCF-7	breast:
2	chr18:29960482..29963119-chr18:29963659..29966463,2	MCF-7	breast:
3	chr18:29952322..29955283-chr18:29962192..29964133,2	K562	blood:

Variant related genes	Relation type
ENSG00000141441	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10502593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10502598	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10502599	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11660076	1.00[CEU][hapmap]
rs11661284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11661378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11661757	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11661767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11663076	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11664951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665544	1.00[CEU][hapmap]
rs11873828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11873865	0.83[JPT][hapmap]
rs11877846	1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11877881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12052010	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1380086	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1458861	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs16962924	1.00[CEU][hapmap]
rs16962941	1.00[CEU][hapmap]
rs16962953	1.00[CEU][hapmap]
rs16962965	1.00[CEU][hapmap]
rs16962971	1.00[CEU][hapmap]
rs16962974	1.00[CEU][hapmap]
rs16962977	1.00[CEU][hapmap]
rs16963129	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs16963184	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17743907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17744164	1.00[CEU][hapmap]
rs17744182	0.83[EUR][1000 genomes]
rs17805881	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17811420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17811474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17811780	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs41535045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4462681	1.00[CEU][hapmap]
rs7236302	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7237059	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7241450	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7243963	1.00[CEU][hapmap]
rs8086990	1.00[CEU][hapmap]
rs9953127	1.00[CEU][hapmap]
rs9960751	1.00[CEU][hapmap]
rs9962307	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29950000-29966200	Weak transcription	Fetal Brain Female	brain
2	chr18:29952800-29963600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:29952800-29964600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:29952800-29973200	Weak transcription	Fetal Stomach	stomach
5	chr18:29953000-29966600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:29953400-29966600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr18:29954000-29974000	Weak transcription	HSMMtube	muscle
8	chr18:29954200-29963200	Weak transcription	HSMM	muscle
9	chr18:29954200-29970800	Weak transcription	Fetal Intestine Large	intestine
10	chr18:29954200-29974400	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:29954400-29972600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr18:29954600-29974200	Weak transcription	Fetal Intestine Small	intestine
13	chr18:29955400-29965400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr18:29955800-29971000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr18:29958000-29965600	Weak transcription	Right Ventricle	heart
16	chr18:29958800-29965200	Weak transcription	Fetal Brain Male	brain
17	chr18:29959000-29966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr18:29959200-29964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr18:29959200-29972600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:29959200-29975400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr18:29959400-29963600	Weak transcription	Liver	Liver
22	chr18:29960600-29966200	Enhancers	Stomach Mucosa	stomach
23	chr18:29960800-29969800	Weak transcription	Small Intestine	intestine
24	chr18:29961400-29964400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr18:29961400-29964400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr18:29961600-29963600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr18:29961600-29964200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr18:29961600-29964200	Enhancers	NHEK	skin
29	chr18:29961800-29963400	Enhancers	Pancreas	Pancrea
30	chr18:29961800-29963600	Enhancers	Ovary	ovary
31	chr18:29961800-29963800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:29961800-29964400	Enhancers	HMEC	breast
33	chr18:29962000-29963800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:29962000-29964200	Enhancers	Adipose Nuclei	Adipose
35	chr18:29962000-29965600	Enhancers	HUVEC	blood vessel
36	chr18:29962200-29963200	Enhancers	Brain Substantia Nigra	brain
37	chr18:29962200-29963400	Enhancers	Brain Cingulate Gyrus	brain
38	chr18:29962200-29963800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr18:29962200-29963800	Enhancers	NH-A	brain
40	chr18:29962200-29964000	Enhancers	HepG2	liver
41	chr18:29962200-29964400	Enhancers	Hela-S3	cervix
42	chr18:29962400-29963400	Enhancers	Stomach Smooth Muscle	stomach
43	chr18:29962400-29964200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr18:29962600-29963400	Enhancers	Osteobl	bone
45	chr18:29962600-29963800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:29962600-29964000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr18:29962800-29963200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr18:29962800-29963200	Weak transcription	Brain Angular Gyrus	brain
49	chr18:29962800-29963200	Weak transcription	Brain Hippocampus Middle	brain
50	chr18:29962800-29963200	Enhancers	A549	lung

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