Variant report

Variant	rs2919129
Chromosome Location	chr2:55216545-55216546
allele	A/C
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	POLR2A	chr2:55212432-55217795	K562	blood:	n/a	n/a
2	POLR2A	chr2:55215917-55217097	A549	lung:	n/a	n/a
3	POLR2A	chr2:55215854-55216822	SK-N-SH	brain:	n/a	n/a
4	E2F4	chr2:55216458-55217015	MCF10A-Er-Src	breast:	n/a	chr2:55216540-55216547 chr2:55216491-55216500

No.	Distal block	Cell Line	Cell type
1	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:
2	chr2:55215896..55218354-chr2:55222752..55225132,2	K562	blood:
3	chr2:55215664..55218100-chr2:55259563..55261709,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10174838	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10210840	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11674808	0.82[EUR][1000 genomes]
rs12464070	0.88[ASN][1000 genomes]
rs12477711	0.91[ASN][1000 genomes]
rs12713284	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13011689	0.84[EUR][1000 genomes]
rs13387751	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2015919	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044291	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255112	0.83[ASW][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255393	0.86[JPT][hapmap]
rs2580764	0.85[ASN][1000 genomes]
rs2580765	0.83[ASW][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2580772	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2580773	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2580776	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588510	0.91[ASW][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588514	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2588517	0.91[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2588518	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2588519	0.82[JPT][hapmap]
rs2588521	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860453	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2902649	0.91[ASN][1000 genomes]
rs2920878	0.92[CEU][hapmap]
rs2920893	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920900	0.82[EUR][1000 genomes]
rs2968786	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968787	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968790	0.82[EUR][1000 genomes]
rs2968793	0.83[EUR][1000 genomes]
rs2968794	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2968795	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968804	0.82[JPT][hapmap]
rs2972072	0.88[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2972075	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2972090	0.86[CHB][hapmap]
rs2972097	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35631428	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35826668	0.95[ASN][1000 genomes]
rs3806570	0.94[ASN][1000 genomes]
rs4672005	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726158	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6755468	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6760429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7340476	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7562292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570629	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7584430	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs968998	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2919129	RTN4	cis	Nerve Tibial	GTEx
rs2919129	RTN4	cis	Esophagus Mucosa	GTEx
rs2919129	RTN4	cis	Whole Blood	GTEx
rs2919129	RTN4	cis	Thyroid	GTEx
rs2919129	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2919129	RTN4	cis	Artery Aorta	GTEx
rs2919129	RTN4	cis	Adipose Subcutaneous	GTEx
rs2919129	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	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
7	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
8	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
9	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
10	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
11	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
12	chr2:55208200-55216600	Weak transcription	Stomach Mucosa	stomach
13	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:55211000-55218600	Weak transcription	Aorta	Aorta
15	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
19	chr2:55213200-55217200	Strong transcription	HSMM	muscle
20	chr2:55213400-55217200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:55213800-55217200	Enhancers	Brain Substantia Nigra	brain
22	chr2:55213800-55226400	Weak transcription	Ovary	ovary
23	chr2:55214000-55216600	Weak transcription	Fetal Lung	lung
24	chr2:55214000-55218600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
26	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
30	chr2:55214600-55225600	Weak transcription	NH-A	brain
31	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:55214800-55216600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:55214800-55216800	Weak transcription	Placenta	Placenta
34	chr2:55214800-55217000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:55214800-55217000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:55214800-55217000	Enhancers	Brain Hippocampus Middle	brain
37	chr2:55214800-55217200	Enhancers	Brain Anterior Caudate	brain
38	chr2:55214800-55217400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:55214800-55217600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:55214800-55218000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:55214800-55218600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55214800-55218600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:55214800-55218600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:55214800-55218600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:55214800-55218600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:55214800-55219000	Weak transcription	NHEK	skin
47	chr2:55214800-55219200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:55214800-55219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:55214800-55220600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links