Variant report

Variant	rs11242990
Chromosome Location	chr6:5107943-5107944
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	chr6:5095410..5098025-chr6:5107266..5109190,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10458182	1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484846	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242991	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242993	0.83[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12110634	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111219	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191255	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192552	0.86[EUR][1000 genomes]
rs12192863	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193229	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195956	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202160	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202384	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203248	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204382	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204490	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206931	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213584	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194957	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17139439	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400671	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392847	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs417629	0.90[AFR][1000 genomes]
rs425930	0.94[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs434350	1.00[ASN][1000 genomes]
rs460111	0.94[CEU][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs467373	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4959330	1.00[ASN][1000 genomes]
rs4959331	1.00[ASN][1000 genomes]
rs4960066	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4960068	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6597114	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911123	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811642	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811643	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761365	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757651	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8980	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs9405800	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405801	0.88[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9504354	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11242990	LYRM4	Cis_1M	lymphoblastoid	RTeQTL
rs11242990	RP11-428J1.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5091000-5108200	Weak transcription	Spleen	Spleen
2	chr6:5091000-5108800	Weak transcription	Right Atrium	heart
3	chr6:5091000-5109000	Weak transcription	Lung	lung
4	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:5096000-5112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:5097200-5108600	Weak transcription	HSMMtube	muscle
7	chr6:5097600-5112800	Weak transcription	K562	blood
8	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
9	chr6:5099000-5108400	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:5099400-5109000	Weak transcription	Right Ventricle	heart
12	chr6:5100600-5109000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:5102800-5110400	Weak transcription	Primary T cells from cord blood	blood
15	chr6:5102800-5111600	Weak transcription	Thymus	Thymus
16	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:5103200-5114000	Weak transcription	Dnd41	blood
19	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:5103400-5108400	Weak transcription	Fetal Lung	lung
21	chr6:5103400-5110600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:5103800-5108800	Weak transcription	Left Ventricle	heart
23	chr6:5103800-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:5103800-5112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:5104200-5112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:5104200-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:5104400-5108200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:5104600-5109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:5105000-5109400	Weak transcription	NHEK	skin
30	chr6:5105000-5113200	Strong transcription	HepG2	liver
31	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:5105800-5125600	Weak transcription	Ovary	ovary
34	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
35	chr6:5106600-5108000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:5106800-5111800	Strong transcription	Fetal Stomach	stomach
37	chr6:5107000-5109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:5107000-5109000	Weak transcription	Placenta	Placenta
39	chr6:5107000-5110800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:5107200-5108000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:5107200-5109400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr6:5107200-5109600	Weak transcription	Gastric	stomach
43	chr6:5107200-5112600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:5107400-5109400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr6:5107400-5110400	Strong transcription	Adipose Nuclei	Adipose
46	chr6:5107600-5109800	Enhancers	Fetal Intestine Large	intestine
47	chr6:5107600-5111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:5107600-5111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:5107800-5108000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:5107800-5108200	Enhancers	Fetal Heart	heart

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