Variant report

Variant	rs11584099
Chromosome Location	chr1:113578412-113578413
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	chr1:113493197..113495739-chr1:113578263..113580046,3	K562	blood:
2	chr1:113577576..113579367-chr1:113585664..113588475,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIG2-5	chr1:113577443-113580582	NONHSAT005312

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11102573	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102577	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102578	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11590174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12066274	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12128904	0.93[ASN][1000 genomes]
rs12129863	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140104	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1216766	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1216772	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216773	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216775	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216779	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216783	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1216784	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1216785	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1216790	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12184285	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12354228	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12740564	0.86[EUR][1000 genomes]
rs12745675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12746771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12754835	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1419136	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1544227	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627925	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17014850	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030901	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17030905	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1728218	0.93[ASN][1000 genomes]
rs1728219	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1728232	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1983929	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2769259	0.89[ASN][1000 genomes]
rs2798687	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2798689	0.89[EUR][1000 genomes]
rs2798691	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798692	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34233065	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34565381	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3889656	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3951437	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4838975	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55894203	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61818171	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818172	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818173	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818174	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61818176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656041	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656311	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71659385	0.83[ASN][1000 genomes]
rs773430	0.86[ASN][1000 genomes]
rs773432	0.86[ASN][1000 genomes]
rs773433	0.86[ASN][1000 genomes]
rs773434	0.87[ASN][1000 genomes]
rs773435	0.86[ASN][1000 genomes]
rs773436	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs773439	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs773440	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9429508	0.86[EUR][1000 genomes]
rs9429509	0.83[EUR][1000 genomes]
rs9429713	0.82[EUR][1000 genomes]
rs9787311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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 target site	59 gene(s)	inside rSNPs	diseases
12	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:113564800-113579400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:113564800-113583000	Weak transcription	Stomach Mucosa	stomach
4	chr1:113570400-113579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:113571200-113579600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:113571400-113579200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:113571600-113579400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:113571600-113584000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:113572000-113579400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:113572600-113579200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:113572600-113579200	Weak transcription	Thymus	Thymus
12	chr1:113572600-113584600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:113573800-113584200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:113574000-113582200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:113574800-113579200	Weak transcription	GM12878-XiMat	blood
16	chr1:113575200-113579400	Weak transcription	HepG2	liver
17	chr1:113577600-113580000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:113577600-113580200	Enhancers	HMEC	breast
19	chr1:113578000-113579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:113578000-113579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:113578000-113579200	Weak transcription	NHDF-Ad	bronchial
22	chr1:113578000-113584800	Weak transcription	Hela-S3	cervix
23	chr1:113578200-113579200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:113578200-113579400	Weak transcription	Osteobl	bone
25	chr1:113578200-113579600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:113578200-113579800	Enhancers	NHEK	skin

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