Variant report

Variant	rs618004
Chromosome Location	chr18:29898479-29898480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29891994..29893877-chr18:29897571..29900006,2	MCF-7	breast:
2	chr18:29895037..29897248-chr18:29897872..29900366,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MEP1B-3	chr18:29898404-29898738	NONHSAT058862

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10502592	0.88[CHB][hapmap]
rs11876773	0.88[CHB][hapmap]
rs1689030	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16963285	0.88[CHB][hapmap]
rs1824304	0.88[CHB][hapmap]
rs594344	0.92[MKK][hapmap];0.86[YRI][hapmap]
rs595792	0.94[CEU][hapmap]
rs598074	0.93[EUR][1000 genomes]
rs606638	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs616601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs619154	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs625361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs638142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs638868	0.85[YRI][hapmap]
rs643836	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs644274	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs656946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs671090	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677721	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs681347	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686196	0.88[CEU][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs687850	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230250	0.88[CHB][hapmap]
rs736218	0.88[CHB][hapmap]
rs8084215	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29868200-29923800	Weak transcription	Gastric	stomach
2	chr18:29889400-29904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr18:29890200-29898800	Weak transcription	Liver	Liver
4	chr18:29890200-29902200	Weak transcription	Spleen	Spleen
5	chr18:29890400-29904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:29891000-29905800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:29891000-29914000	Weak transcription	Fetal Brain Female	brain
8	chr18:29891200-29905600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:29893400-29903200	Weak transcription	Pancreas	Pancrea
10	chr18:29895800-29898600	Enhancers	Brain Cingulate Gyrus	brain
11	chr18:29895800-29898800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr18:29895800-29898800	Enhancers	Osteobl	bone
13	chr18:29896000-29899200	Enhancers	Brain Substantia Nigra	brain
14	chr18:29896400-29899200	Enhancers	Fetal Muscle Leg	muscle
15	chr18:29896600-29900000	Enhancers	Adipose Nuclei	Adipose
16	chr18:29896800-29899800	Enhancers	HepG2	liver
17	chr18:29897000-29898600	Weak transcription	Aorta	Aorta
18	chr18:29897000-29898800	Enhancers	Fetal Lung	lung
19	chr18:29897200-29898600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr18:29897200-29898800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr18:29897200-29899000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr18:29897200-29899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:29897200-29903200	Weak transcription	Psoas Muscle	Psoas
24	chr18:29897200-29903400	Weak transcription	Right Ventricle	heart
25	chr18:29897200-29918800	Weak transcription	Fetal Intestine Large	intestine
26	chr18:29897200-29926400	Weak transcription	Fetal Stomach	stomach
27	chr18:29897400-29898600	Weak transcription	Lung	lung
28	chr18:29897400-29899000	Enhancers	HSMMtube	muscle
29	chr18:29897400-29899600	Enhancers	Brain Hippocampus Middle	brain
30	chr18:29897400-29909000	Weak transcription	Left Ventricle	heart
31	chr18:29897400-29923800	Weak transcription	Esophagus	oesophagus
32	chr18:29897400-29923800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr18:29897800-29898600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:29897800-29899000	Enhancers	NHDF-Ad	bronchial
35	chr18:29897800-29901800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr18:29898000-29898600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr18:29898000-29898600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr18:29898000-29899200	Enhancers	HSMM	muscle
39	chr18:29898000-29899800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:29898000-29906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr18:29898000-29906400	Weak transcription	Small Intestine	intestine
42	chr18:29898000-29906600	Weak transcription	Brain Angular Gyrus	brain
43	chr18:29898000-29918600	Weak transcription	Fetal Intestine Small	intestine
44	chr18:29898200-29898800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:29898200-29899000	Enhancers	Placenta Amnion	Placenta Amnion
46	chr18:29898200-29899200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr18:29898200-29899400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr18:29898200-29901400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:29898200-29902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr18:29898200-29915400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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