Variant report

Variant	rs11958835
Chromosome Location	chr5:98268026-98268027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
2	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:
3	chr5:98265027..98268409-chr5:98365166..98367986,4	K562	blood:
4	chr5:98266485..98269344-chr6:26198000..26199535,2	MCF-7	breast:
5	chr5:98266316..98268754-chr5:98386981..98389928,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-1	chr5:98264861-98270036	NONHSAT102968

Variant related genes	Relation type
ENSG00000197409	Chromatin interaction
ENSG00000200351	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000241597	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10039507	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10041263	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10041335	0.83[EUR][1000 genomes]
rs10055595	0.83[EUR][1000 genomes]
rs10056842	0.83[EUR][1000 genomes]
rs10056918	0.83[EUR][1000 genomes]
rs10061406	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10064594	0.81[EUR][1000 genomes]
rs10065808	0.83[EUR][1000 genomes]
rs10067635	0.83[EUR][1000 genomes]
rs10067866	0.83[EUR][1000 genomes]
rs10068003	0.83[EUR][1000 genomes]
rs10068917	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs10077697	1.00[CEU][hapmap]
rs10085106	1.00[CEU][hapmap]
rs10085145	1.00[CEU][hapmap]
rs10515284	1.00[CEU][hapmap]
rs11948998	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952820	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11953096	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12332280	0.83[EUR][1000 genomes]
rs12332340	0.83[EUR][1000 genomes]
rs12332364	0.81[EUR][1000 genomes]
rs12332383	0.83[EUR][1000 genomes]
rs161742	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17166414	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17166423	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17166428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17166439	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17166455	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17166484	0.87[EUR][1000 genomes]
rs17166575	0.83[EUR][1000 genomes]
rs17166578	0.89[CEU][hapmap]
rs17663317	0.90[CEU][hapmap]
rs2164986	0.93[EUR][1000 genomes]
rs2963709	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3179904	1.00[CEU][hapmap]
rs327810	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36011435	0.93[EUR][1000 genomes]
rs44070	0.85[EUR][1000 genomes]
rs55780476	0.83[EUR][1000 genomes]
rs55821667	0.83[EUR][1000 genomes]
rs55854720	0.81[EUR][1000 genomes]
rs55862038	0.81[ASN][1000 genomes]
rs56086412	0.83[EUR][1000 genomes]
rs56096102	0.81[EUR][1000 genomes]
rs56115002	0.83[EUR][1000 genomes]
rs56153113	0.83[EUR][1000 genomes]
rs56159022	0.81[EUR][1000 genomes]
rs56160758	0.83[EUR][1000 genomes]
rs56232429	0.81[EUR][1000 genomes]
rs56331326	0.89[EUR][1000 genomes]
rs56331947	0.87[EUR][1000 genomes]
rs56400831	0.93[EUR][1000 genomes]
rs56898185	0.81[ASN][1000 genomes]
rs58224759	0.81[ASN][1000 genomes]
rs58479016	0.83[EUR][1000 genomes]
rs59181854	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59325325	0.81[ASN][1000 genomes]
rs61199566	0.81[ASN][1000 genomes]
rs6596551	0.81[ASN][1000 genomes]
rs6866527	1.00[CEU][hapmap]
rs6866629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880359	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883467	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6890358	0.83[EUR][1000 genomes]
rs6893282	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6895358	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs727637	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776004	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776005	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776017	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73776026	1.00[ASN][1000 genomes]
rs73776027	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73776028	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73776032	1.00[ASN][1000 genomes]
rs7708436	0.87[EUR][1000 genomes]
rs7726329	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7737402	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs9327950	0.83[EUR][1000 genomes]
rs9327954	0.83[EUR][1000 genomes]
rs9327955	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98268200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:98266000-98269400	Weak transcription	Pancreas	Pancrea
3	chr5:98266000-98269800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:98266000-98271000	Weak transcription	Left Ventricle	heart
5	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
6	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
8	chr5:98266200-98268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:98266200-98269000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:98266200-98269400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
13	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
15	chr5:98266400-98269000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:98266400-98269200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:98266400-98270400	Weak transcription	HSMMtube	muscle
18	chr5:98266400-98270600	Weak transcription	NH-A	brain
19	chr5:98266400-98270600	Weak transcription	NHLF	lung
20	chr5:98266400-98270800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:98266400-98271000	Weak transcription	Psoas Muscle	Psoas
22	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
31	chr5:98266600-98268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:98266600-98268800	Weak transcription	NHEK	skin
33	chr5:98266600-98269000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:98266600-98269200	Weak transcription	Right Atrium	heart
35	chr5:98266600-98270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:98266600-98270200	Weak transcription	Osteobl	bone
37	chr5:98266600-98270400	Weak transcription	A549	lung
38	chr5:98266600-98270400	Weak transcription	HSMM	muscle
39	chr5:98266600-98270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:98266600-98272000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr5:98266600-98273400	Weak transcription	NHDF-Ad	bronchial
42	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
43	chr5:98266800-98268600	Weak transcription	Liver	Liver
44	chr5:98266800-98268800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:98266800-98268800	Weak transcription	Thymus	Thymus
46	chr5:98266800-98269000	Weak transcription	Brain Angular Gyrus	brain
47	chr5:98266800-98269600	Weak transcription	Fetal Brain Male	brain
48	chr5:98266800-98270400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:98266800-98270600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:98266800-98273200	Weak transcription	HUVEC	blood vessel

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