Variant report

Variant	rs1880075
Chromosome Location	chr2:50346988-50346989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1037428	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490240	0.91[ASN][1000 genomes]
rs10865243	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125288	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125289	0.91[ASN][1000 genomes]
rs11125290	0.91[ASN][1000 genomes]
rs11125291	0.91[ASN][1000 genomes]
rs11125292	0.91[ASN][1000 genomes]
rs11125294	0.88[ASN][1000 genomes]
rs11883844	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11887484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898302	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901625	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151722	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12151727	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465888	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12468151	0.91[ASN][1000 genomes]
rs12468252	0.88[ASN][1000 genomes]
rs12468342	0.89[ASN][1000 genomes]
rs12468396	0.89[ASN][1000 genomes]
rs12469244	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473119	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12474335	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12477934	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12478732	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12479057	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613266	0.94[ASN][1000 genomes]
rs12613778	0.84[EUR][1000 genomes]
rs12620250	0.93[ASN][1000 genomes]
rs12622844	0.94[ASN][1000 genomes]
rs12622858	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1452768	0.85[AFR][1000 genomes]
rs1452778	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1452779	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1452780	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1452781	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1452783	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1517827	0.88[ASN][1000 genomes]
rs1563024	0.88[ASN][1000 genomes]
rs1563026	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1563027	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1584763	0.88[ASN][1000 genomes]
rs17039801	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17039807	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17039848	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17039863	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17039900	1.00[ASN][1000 genomes]
rs17039905	0.94[ASN][1000 genomes]
rs17039932	0.93[ASN][1000 genomes]
rs17039935	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17039940	0.93[ASN][1000 genomes]
rs17039947	0.91[ASN][1000 genomes]
rs17039985	0.90[ASN][1000 genomes]
rs1840074	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961358	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2011317	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2045003	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34350062	0.82[EUR][1000 genomes]
rs4032305	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4641977	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4971554	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4971556	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971648	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971649	0.89[ASN][1000 genomes]
rs57366806	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61035060	0.91[ASN][1000 genomes]
rs6716404	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6731360	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72874683	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72874698	0.91[ASN][1000 genomes]
rs72878115	0.84[EUR][1000 genomes]
rs72878120	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72878122	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72878124	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72878157	0.94[ASN][1000 genomes]
rs72878159	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72881242	0.90[ASN][1000 genomes]
rs7590544	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7607863	0.91[ASN][1000 genomes]
rs896683	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896684	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921572	0.84[EUR][1000 genomes]
rs921573	0.84[EUR][1000 genomes]
rs930752	0.86[AFR][1000 genomes]
rs9917277	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2756107	chr2:50307245-50440043	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948833	chr2:50307245-50459077	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2756536	chr2:50313811-50375695	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1002344	chr2:50326207-50518933	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535692	chr2:50326207-50518933	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50337400-50349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:50343200-50347200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr2:50344600-50349400	Weak transcription	Fetal Brain Female	brain
4	chr2:50344600-50352400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:50345200-50347200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:50345200-50354200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:50345600-50347600	Enhancers	Fetal Brain Male	brain
8	chr2:50345800-50347200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:50345800-50347600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:50346000-50347600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:50346000-50347800	Weak transcription	Stomach Mucosa	stomach
12	chr2:50346000-50349000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:50346000-50349200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:50346200-50349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:50346400-50347000	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr2:50346400-50347200	Weak transcription	Brain Germinal Matrix	brain
17	chr2:50346600-50347200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr2:50346600-50347600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:50346800-50347000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr2:50346800-50349200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links