Variant report

Variant	rs968998
Chromosome Location	chr2:55238851-55238852
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:55238695-55239263	HepG2	liver:	n/a	n/a
2	SPI1	chr2:55238685-55239130	HL-60	blood:	n/a	chr2:55238890-55238903 chr2:55238890-55238903 chr2:55238891-55238904
3	POLR2A	chr2:55222320-55241658	K562	blood:	n/a	n/a
4	TEAD4	chr2:55238608-55239335	HepG2	liver:	n/a	n/a
5	SPI1	chr2:55238753-55239123	HL-60	blood:	n/a	chr2:55238890-55238903 chr2:55238890-55238903 chr2:55238891-55238904

No.	Distal block	Cell Line	Cell type
1	chr2:55238547..55240641-chr2:55252176..55254092,2	MCF-7	breast:
2	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:
3	chr2:55224190..55226193-chr2:55238312..55240025,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10174838	0.93[ASN][1000 genomes]
rs10210840	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12464070	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12477711	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12713284	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs13387751	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2015919	0.84[ASN][1000 genomes]
rs2044291	0.85[ASN][1000 genomes]
rs2255112	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2580765	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2580772	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2580776	0.90[ASN][1000 genomes]
rs2588510	0.95[CHB][hapmap]
rs2588517	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2588518	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs2588519	0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2588521	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2860453	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs2902649	0.85[ASN][1000 genomes]
rs2919129	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968786	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2968787	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs2968791	0.86[AMR][1000 genomes]
rs2968804	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2972090	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972097	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs35631428	0.88[ASN][1000 genomes]
rs35826668	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3806570	0.91[ASN][1000 genomes]
rs4672005	0.85[ASN][1000 genomes]
rs6545466	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs6713935	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs6726158	0.94[ASN][1000 genomes]
rs6755468	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs6760429	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs7340476	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7562292	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs7570629	0.95[CHB][hapmap]
rs7584430	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs968998	RTN4	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55227600-55239000	Weak transcription	Hela-S3	cervix
3	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:55233200-55240400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:55235600-55240600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:55236200-55239600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:55236600-55241400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:55236800-55240800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:55237200-55239600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:55237200-55241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr2:55237400-55239400	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:55237400-55240800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
18	chr2:55237600-55239000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:55237600-55239000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:55237600-55239000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55237600-55239000	Enhancers	Aorta	Aorta
22	chr2:55237600-55239000	Enhancers	Brain Anterior Caudate	brain
23	chr2:55237600-55239200	Enhancers	Fetal Muscle Leg	muscle
24	chr2:55237600-55239400	Enhancers	HSMM	muscle
25	chr2:55237600-55239600	Enhancers	NHEK	skin
26	chr2:55237600-55239800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:55237600-55239800	Weak transcription	Brain Angular Gyrus	brain
28	chr2:55237600-55240000	Enhancers	Dnd41	blood
29	chr2:55237600-55240400	Weak transcription	Fetal Brain Male	brain
30	chr2:55237600-55240800	Enhancers	Colon Smooth Muscle	Colon
31	chr2:55237600-55241000	Enhancers	NH-A	brain
32	chr2:55237600-55241200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:55237600-55241400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:55237600-55241400	Enhancers	Fetal Lung	lung
35	chr2:55237600-55241600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
40	chr2:55237600-55249600	Weak transcription	Gastric	stomach
41	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:55237600-55258600	Weak transcription	Ovary	ovary
43	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
44	chr2:55237800-55239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:55237800-55239000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr2:55237800-55239000	Weak transcription	Colonic Mucosa	Colon
47	chr2:55237800-55239000	Enhancers	Fetal Intestine Large	intestine
48	chr2:55237800-55239200	Enhancers	Primary B cells from cord blood	blood
49	chr2:55237800-55239200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:55237800-55239200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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