Variant report

Variant	rs170579
Chromosome Location	chr5:98269012-98269013
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	chr5:98261995..98270397-chr5:98280624..98292060,15	K562	blood:
2	chr5:98266485..98269344-chr6:26198000..26199535,2	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
ENSG00000241597	Chromatin interaction
ENSG00000196866	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044680	1.00[EUR][1000 genomes]
rs10045317	1.00[EUR][1000 genomes]
rs10046011	1.00[EUR][1000 genomes]
rs10060286	1.00[EUR][1000 genomes]
rs13358830	1.00[EUR][1000 genomes]
rs1382336	1.00[EUR][1000 genomes]
rs161743	0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162139	1.00[EUR][1000 genomes]
rs162141	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162142	1.00[EUR][1000 genomes]
rs162143	1.00[EUR][1000 genomes]
rs162157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162160	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162161	1.00[AMR][1000 genomes]
rs162162	0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166397	1.00[EUR][1000 genomes]
rs17166450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166454	0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs179175	1.00[EUR][1000 genomes]
rs1828171	1.00[EUR][1000 genomes]
rs28782775	1.00[EUR][1000 genomes]
rs325196	1.00[AMR][1000 genomes]
rs325198	1.00[EUR][1000 genomes]
rs325210	1.00[AMR][1000 genomes]
rs325216	1.00[EUR][1000 genomes]
rs327801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327805	1.00[EUR][1000 genomes]
rs451883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57969582	1.00[EUR][1000 genomes]
rs59156696	1.00[EUR][1000 genomes]
rs61578983	1.00[EUR][1000 genomes]
rs6891520	1.00[EUR][1000 genomes]
rs73151499	1.00[EUR][1000 genomes]
rs73153514	1.00[EUR][1000 genomes]
rs73153532	1.00[EUR][1000 genomes]
rs73155421	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73155423	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7727696	1.00[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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98269400	Weak transcription	Pancreas	Pancrea
2	chr5:98266000-98269800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:98266000-98271000	Weak transcription	Left Ventricle	heart
4	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
5	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
7	chr5:98266200-98269400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
10	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
12	chr5:98266400-98269200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:98266400-98270400	Weak transcription	HSMMtube	muscle
14	chr5:98266400-98270600	Weak transcription	NH-A	brain
15	chr5:98266400-98270600	Weak transcription	NHLF	lung
16	chr5:98266400-98270800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:98266400-98271000	Weak transcription	Psoas Muscle	Psoas
18	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
27	chr5:98266600-98269200	Weak transcription	Right Atrium	heart
28	chr5:98266600-98270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:98266600-98270200	Weak transcription	Osteobl	bone
30	chr5:98266600-98270400	Weak transcription	A549	lung
31	chr5:98266600-98270400	Weak transcription	HSMM	muscle
32	chr5:98266600-98270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:98266600-98272000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:98266600-98273400	Weak transcription	NHDF-Ad	bronchial
35	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
36	chr5:98266800-98269600	Weak transcription	Fetal Brain Male	brain
37	chr5:98266800-98270400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:98266800-98270600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:98266800-98273200	Weak transcription	HUVEC	blood vessel
40	chr5:98266800-98274000	Weak transcription	Fetal Lung	lung
41	chr5:98266800-98277000	Weak transcription	HMEC	breast
42	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
43	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:98267000-98269800	Weak transcription	Dnd41	blood
45	chr5:98267000-98274000	Weak transcription	Adipose Nuclei	Adipose
46	chr5:98267200-98269400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:98267200-98269800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:98267200-98270200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:98267200-98270200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:98267200-98270600	Weak transcription	Fetal Brain Female	brain

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