Variant report

Variant	rs2949813
Chromosome Location	chr2:54024957-54024958
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54016706..54018881-chr2:54023439..54026014,2	K562	blood:
2	chr2:53994110..53996548-chr2:54024126..54025670,2	K562	blood:

Variant related genes	Relation type
ENSG00000143942	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10490468	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs11897282	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs11901698	0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs1232	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs13408029	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17045176	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045203	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17520505	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17520854	0.87[AMR][1000 genomes]
rs17521008	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2008082	0.84[AFR][1000 genomes]
rs2287340	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2302797	0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2542572	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2542573	0.87[ASN][1000 genomes]
rs2542578	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2542580	0.92[ASN][1000 genomes]
rs2542581	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs2542582	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2542583	0.86[ASN][1000 genomes]
rs2542589	0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2542590	0.91[ASN][1000 genomes]
rs2542591	0.85[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs2542592	0.92[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs2543629	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2692512	0.95[ASN][1000 genomes]
rs2692513	0.95[ASN][1000 genomes]
rs2692519	0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.92[ASN][1000 genomes]
rs2692521	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2692522	0.89[ASN][1000 genomes]
rs2692523	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2692533	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2692535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2909262	0.85[ASN][1000 genomes]
rs2949814	0.83[ASN][1000 genomes]
rs35772199	0.83[ASN][1000 genomes]
rs3731970	0.82[YRI][hapmap]
rs3770394	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770395	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770397	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770399	0.88[ASN][1000 genomes]
rs3770407	0.81[YRI][hapmap]
rs3770411	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs3922262	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4116709	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs55897904	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58326257	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62137573	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137602	0.85[ASN][1000 genomes]
rs62137606	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137610	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137611	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62137612	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6730006	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs719127	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs72901256	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7600817	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs805316	0.92[CHB][hapmap]
rs805334	0.90[CHB][hapmap]
rs805338	0.92[CHB][hapmap]
rs805368	0.85[ASN][1000 genomes]
rs805383	0.86[ASN][1000 genomes]
rs805385	0.86[ASN][1000 genomes]
rs805398	0.82[ASN][1000 genomes]
rs805435	0.92[ASN][1000 genomes]
rs805437	0.92[CHB][hapmap];0.88[ASN][1000 genomes]
rs805446	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs805447	0.92[CHB][hapmap]
rs805449	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv963914	chr2:54021710-54028552	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
3	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
4	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
6	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
7	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:54015800-54025000	Weak transcription	Right Ventricle	heart
13	chr2:54015800-54025200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:54015800-54026000	Weak transcription	Fetal Brain Male	brain
15	chr2:54015800-54028600	Weak transcription	HMEC	breast
16	chr2:54015800-54029400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:54015800-54029600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:54015800-54029800	Weak transcription	Psoas Muscle	Psoas
19	chr2:54015800-54029800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:54015800-54038400	Weak transcription	Fetal Heart	heart
21	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:54016000-54031600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:54016200-54028600	Weak transcription	Colon Smooth Muscle	Colon
24	chr2:54016400-54025400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:54016400-54043000	Weak transcription	Gastric	stomach
26	chr2:54016800-54025000	Weak transcription	Spleen	Spleen
27	chr2:54017400-54031000	Weak transcription	Ovary	ovary
28	chr2:54017800-54027400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:54020200-54025000	Weak transcription	Pancreas	Pancrea
30	chr2:54020200-54029600	Weak transcription	Brain Angular Gyrus	brain
31	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
32	chr2:54020400-54025800	Weak transcription	NHLF	lung
33	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:54020600-54048600	Strong transcription	Osteobl	bone
36	chr2:54020800-54025000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:54021000-54027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:54021000-54029200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:54021000-54030600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:54021000-54030600	Strong transcription	HepG2	liver
41	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:54021200-54030000	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:54021200-54030600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
48	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus

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