Variant report

Variant	rs7570629
Chromosome Location	chr2:55255935-55255936
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55253687..55256302-chr2:55275288..55279077,3	K562	blood:
2	chr2:55255815..55260220-chr2:55273453..55278520,8	MCF-7	breast:
3	chr2:55255186..55258524-chr2:55346221..55348339,3	K562	blood:
4	chr2:55252582..55260799-chr2:55274165..55279100,17	MCF-7	breast:
5	chr2:55253309..55255989-chr2:55259127..55262322,3	MCF-7	breast:
6	chr2:55255745..55260236-chr2:55263069..55266549,5	K562	blood:
7	chr2:55254227..55256679-chr2:55395838..55397468,2	K562	blood:
8	chr2:55255325..55257378-chr2:55267721..55270534,4	MCF-7	breast:
9	chr2:55253656..55256107-chr2:55260589..55262893,2	K562	blood:
10	chr2:55253484..55256107-chr2:55261121..55262893,2	K562	blood:
11	chr2:55246557..55249520-chr2:55255135..55258063,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10174838	0.84[AMR][1000 genomes]
rs10210840	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12713284	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs13387751	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2044291	0.83[AMR][1000 genomes]
rs2255112	1.00[JPT][hapmap]
rs2255393	0.91[JPT][hapmap]
rs2580765	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2580772	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs2580776	0.80[AMR][1000 genomes]
rs2588510	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2588517	0.95[CHB][hapmap]
rs2588518	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2588519	0.86[JPT][hapmap]
rs2588521	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2860453	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2919129	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2920878	0.93[CEU][hapmap]
rs2920893	0.81[AMR][1000 genomes]
rs2968786	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968787	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2968794	0.92[CEU][hapmap]
rs2968795	0.93[CEU][hapmap]
rs2968804	0.87[JPT][hapmap]
rs2972072	0.88[CEU][hapmap]
rs2972075	0.88[CEU][hapmap]
rs2972090	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2972097	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs35631428	0.81[ASN][1000 genomes]
rs4672005	0.81[AMR][1000 genomes]
rs6545466	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs6755468	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs6760429	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7340476	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs7562292	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs968998	0.95[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7570629	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs7570629	RTN4	cis	Artery Tibial	GTEx
rs7570629	RTN4	cis	Thyroid	GTEx
rs7570629	RTN4	cis	Adipose Subcutaneous	GTEx
rs7570629	RTN4	cis	Esophagus Mucosa	GTEx
rs7570629	RTN4	cis	Nerve Tibial	GTEx
rs7570629	RTN4	cis	Artery Aorta	GTEx
rs7570629	RTN4	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
5	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
7	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55245000-55256000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
10	chr2:55246800-55259800	Weak transcription	NH-A	brain
11	chr2:55248200-55258400	Weak transcription	Lung	lung
12	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:55248600-55256400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:55249000-55256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr2:55249000-55256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:55249000-55256600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:55249000-55256600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr2:55249000-55256600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:55249200-55256600	Enhancers	Brain Angular Gyrus	brain
20	chr2:55249400-55256400	Enhancers	Adipose Nuclei	Adipose
21	chr2:55250000-55256000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:55250000-55256400	Enhancers	Colon Smooth Muscle	Colon
23	chr2:55250000-55260000	Weak transcription	Gastric	stomach
24	chr2:55250200-55256400	Enhancers	Rectal Smooth Muscle	rectum
25	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
27	chr2:55250600-55258400	Weak transcription	Spleen	Spleen
28	chr2:55251400-55258000	Weak transcription	Fetal Heart	heart
29	chr2:55251400-55259400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:55251600-55256200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:55251600-55256600	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:55251800-55256000	Enhancers	Primary T cells from cord blood	blood
33	chr2:55251800-55256400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr2:55252200-55256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:55252200-55256600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:55252200-55257000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:55252400-55256200	Enhancers	HepG2	liver
38	chr2:55252400-55257200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:55252400-55259000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr2:55252600-55258400	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:55252600-55261400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr2:55252800-55256400	Genic enhancers	A549	lung
43	chr2:55253200-55256400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:55253200-55256800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:55253400-55256400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:55253400-55256400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:55253400-55257000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr2:55253400-55257400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:55253600-55256000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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