Variant report

Variant	rs7241650
Chromosome Location	chr18:12880533-12880534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12875420..12877466-chr18:12879544..12881307,2	MCF-7	breast:
2	chr18:12862494..12865307-chr18:12880258..12883236,3	MCF-7	breast:
3	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
4	chr18:12833814..12836436-chr18:12879380..12882256,2	MCF-7	breast:
5	chr18:12880282..12884361-chr18:12946145..12949673,9	K562	blood:
6	chr18:12712618..12714597-chr18:12880301..12882265,2	K562	blood:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2032174	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap]
rs2292758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2847288	0.95[CHD][hapmap];0.89[JPT][hapmap]
rs3826556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs45579734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797707	0.82[ASN][1000 genomes]
rs4797708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487273	1.00[YRI][hapmap]
rs507304	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs513185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs547268	0.92[YRI][hapmap]
rs56384328	0.88[ASN][1000 genomes]
rs578377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58200120	0.85[ASN][1000 genomes]
rs59471125	0.85[ASN][1000 genomes]
rs607906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60803113	0.88[ASN][1000 genomes]
rs622717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657555	1.00[ASW][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs669822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs670671	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683468	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7238238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872144	0.87[ASN][1000 genomes]
rs73950681	0.83[ASN][1000 genomes]
rs73950683	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73950684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73950685	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8084365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8098730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961827	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961931	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
2	chr18:12863400-12881400	Weak transcription	Right Atrium	heart
3	chr18:12863600-12882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:12865000-12881800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:12865800-12883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:12872400-12881600	Weak transcription	Ovary	ovary
7	chr18:12875600-12882800	Enhancers	Primary B cells from peripheral blood	blood
8	chr18:12875800-12882000	Weak transcription	HSMM	muscle
9	chr18:12876000-12882000	Weak transcription	Fetal Intestine Large	intestine
10	chr18:12876400-12881200	Weak transcription	Fetal Muscle Leg	muscle
11	chr18:12877400-12881600	Weak transcription	Fetal Intestine Small	intestine
12	chr18:12877600-12881600	Weak transcription	Right Ventricle	heart
13	chr18:12877600-12882200	Weak transcription	Fetal Heart	heart
14	chr18:12877800-12882400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr18:12878000-12882600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr18:12878200-12882400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr18:12878400-12882000	Enhancers	HepG2	liver
18	chr18:12878600-12881200	Enhancers	Spleen	Spleen
19	chr18:12878600-12881400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr18:12878600-12882600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr18:12878600-12882600	Enhancers	Duodenum Mucosa	Duodenum
22	chr18:12878600-12882800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr18:12878600-12882800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr18:12878800-12882400	Flanking Active TSS	GM12878-XiMat	blood
25	chr18:12878800-12882600	Enhancers	Primary T cells from cord blood	blood
26	chr18:12878800-12882600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr18:12878800-12882600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr18:12878800-12882600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr18:12878800-12882800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr18:12879000-12880800	Enhancers	Osteobl	bone
31	chr18:12879000-12881600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr18:12879000-12882600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr18:12879000-12882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr18:12879200-12880600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr18:12879200-12880600	Enhancers	Left Ventricle	heart
36	chr18:12879200-12880800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr18:12879200-12880800	Enhancers	Adipose Nuclei	Adipose
38	chr18:12879200-12881400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12879200-12881600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:12879200-12882000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr18:12879200-12882000	Enhancers	HMEC	breast
42	chr18:12879200-12882800	Enhancers	Liver	Liver
43	chr18:12879400-12880800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr18:12879400-12881800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr18:12879400-12881800	Weak transcription	A549	lung
46	chr18:12879600-12881400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr18:12879600-12882000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr18:12879600-12882200	Weak transcription	Fetal Kidney	kidney
49	chr18:12879600-12882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr18:12879600-12883200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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