Variant report

Variant	rs1403900
Chromosome Location	chr2:168199991-168199992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10186558	0.86[EUR][1000 genomes]
rs10189334	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10192896	0.90[EUR][1000 genomes]
rs10497321	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs10803821	0.83[EUR][1000 genomes]
rs10803822	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10930264	0.85[EUR][1000 genomes]
rs10930265	0.87[EUR][1000 genomes]
rs10930268	0.85[EUR][1000 genomes]
rs10930270	0.85[EUR][1000 genomes]
rs12105767	0.86[EUR][1000 genomes]
rs12620530	0.83[EUR][1000 genomes]
rs12692859	0.85[EUR][1000 genomes]
rs1357599	0.87[EUR][1000 genomes]
rs1357605	0.84[EUR][1000 genomes]
rs1382318	0.85[EUR][1000 genomes]
rs1403894	0.87[EUR][1000 genomes]
rs1403897	0.85[EUR][1000 genomes]
rs1403898	0.85[EUR][1000 genomes]
rs1403899	0.85[EUR][1000 genomes]
rs1403901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478384	0.85[EUR][1000 genomes]
rs1478385	0.85[EUR][1000 genomes]
rs1523878	0.86[EUR][1000 genomes]
rs1523882	0.85[EUR][1000 genomes]
rs1540820	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1540821	0.91[EUR][1000 genomes]
rs1540822	0.86[EUR][1000 genomes]
rs1568747	0.85[EUR][1000 genomes]
rs1581484	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581485	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1589728	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1608519	0.85[EUR][1000 genomes]
rs1608520	0.85[EUR][1000 genomes]
rs16853227	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs16853282	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs16853285	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs16853291	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs16853296	0.84[CEU][hapmap]
rs16853305	0.91[CEU][hapmap]
rs16853306	0.83[CEU][hapmap]
rs16853309	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs16853328	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs16853331	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs16853337	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs16853344	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs16853370	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1851758	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1851759	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1851760	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1916742	0.88[EUR][1000 genomes]
rs1916746	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1916747	0.86[EUR][1000 genomes]
rs1916748	0.85[EUR][1000 genomes]
rs1916749	0.85[EUR][1000 genomes]
rs1916750	0.85[EUR][1000 genomes]
rs1916751	0.85[EUR][1000 genomes]
rs1996949	0.85[EUR][1000 genomes]
rs2103098	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2140501	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2177441	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177442	0.88[EUR][1000 genomes]
rs2204280	0.80[EUR][1000 genomes]
rs2250619	0.85[EUR][1000 genomes]
rs2617368	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617386	0.85[EUR][1000 genomes]
rs2617388	0.85[EUR][1000 genomes]
rs2617391	0.85[EUR][1000 genomes]
rs2617393	0.85[EUR][1000 genomes]
rs2617394	0.85[EUR][1000 genomes]
rs2617398	0.85[EUR][1000 genomes]
rs2617399	0.85[EUR][1000 genomes]
rs2689820	0.85[EUR][1000 genomes]
rs2689823	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2689825	0.85[EUR][1000 genomes]
rs2689826	0.85[EUR][1000 genomes]
rs2689827	0.85[EUR][1000 genomes]
rs2689828	0.85[EUR][1000 genomes]
rs2689832	0.85[EUR][1000 genomes]
rs2689833	0.85[EUR][1000 genomes]
rs2689842	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2927600	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2949009	0.85[EUR][1000 genomes]
rs2949010	0.85[EUR][1000 genomes]
rs3749004	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs3749006	0.83[CEU][hapmap]
rs4538166	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4667949	0.85[EUR][1000 genomes]
rs57797869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58013803	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60102532	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61529696	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6432987	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs6726067	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6743941	0.95[ASN][1000 genomes]
rs6746887	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6747227	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs6759681	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs73972228	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73972230	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573953	0.83[CEU][hapmap]
rs7576187	0.85[EUR][1000 genomes]
rs7576938	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs7580183	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs7581012	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs7581190	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs7593641	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7594496	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7600424	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs7602259	0.84[JPT][hapmap]
rs7607246	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs899185	0.85[EUR][1000 genomes]
rs922536	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs922537	0.91[CEU][hapmap]
rs9287881	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940315	0.85[EUR][1000 genomes]
rs9751663	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9751666	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875377	chr2:168084857-168203116	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv875378	chr2:168107491-168297961	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3364733	chr2:168109919-168302141	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:168193600-168200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:168194000-168201600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:168194200-168211600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:168197800-168202200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:168198000-168203000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:168199000-168201800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr2:168199200-168200000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:168199200-168200400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:168199200-168201200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:168199200-168201200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:168199200-168202400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:168199200-168202400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:168199200-168202800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:168199200-168209000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:168199400-168200000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:168199400-168200600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:168199600-168200600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:168199600-168221400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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