Variant report

Variant	rs2428416
Chromosome Location	chr7:27069689-27069690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:27061277-27071265..7:27203007-27207968	H1-hESC	embryonic stem cell:	embryo
2	7:27061277-27071265..7:27238414-27242313	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000078399	Chromatin interaction
ENSG00000106031	Chromatin interaction
ENSG00000243766	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10227231	0.90[JPT][hapmap]
rs10227553	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10238645	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10242572	0.90[JPT][hapmap]
rs10242754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10244751	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10248684	0.82[EUR][1000 genomes]
rs10256250	0.90[JPT][hapmap]
rs10270187	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10272190	0.90[JPT][hapmap]
rs10272457	0.90[JPT][hapmap]
rs10486483	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10486485	0.90[JPT][hapmap]
rs11563327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12530718	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12534899	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs12534901	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12534912	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12535784	0.90[JPT][hapmap]
rs12540388	0.90[JPT][hapmap]
rs17323934	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs17377696	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17436410	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17471061	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17471088	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030136	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2031811	0.89[JPT][hapmap]
rs2079138	0.88[EUR][1000 genomes]
rs2248744	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2254463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2264802	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2264803	0.93[ASN][1000 genomes]
rs2391362	0.90[JPT][hapmap]
rs2428417	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2428418	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2428421	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2428425	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2428431	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2462900	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2462902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2462904	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2462906	0.86[EUR][1000 genomes]
rs2462908	0.89[EUR][1000 genomes]
rs2462910	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465270	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2465271	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465274	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2522824	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2522825	0.86[EUR][1000 genomes]
rs2522826	0.87[EUR][1000 genomes]
rs2648076	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2693659	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2693662	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2693665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2693668	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2712234	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs2712238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712242	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712244	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712245	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712246	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2712248	0.87[EUR][1000 genomes]
rs2712250	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3801803	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs3801805	0.90[JPT][hapmap]
rs3801807	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs3801808	0.90[JPT][hapmap]
rs3801810	0.90[JPT][hapmap]
rs3801812	0.90[JPT][hapmap]
rs3801813	0.90[JPT][hapmap]
rs3801814	0.90[JPT][hapmap]
rs3801815	0.90[JPT][hapmap]
rs3801816	0.90[JPT][hapmap]
rs55889667	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56144845	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6461979	0.90[JPT][hapmap]
rs7791513	0.90[JPT][hapmap]
rs7804356	0.88[CHB][hapmap];0.89[JPT][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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv967485	chr7:27066773-27082518	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2428416	HOXA2	cis	Whole Blood	GTEx
rs2428416	HOTAIRM1	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27065200-27070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:27068200-27071600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:27068400-27071800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr7:27068600-27071600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:27068800-27069800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:27068800-27069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:27068800-27070200	Weak transcription	HSMMtube	muscle
8	chr7:27068800-27070400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:27068800-27071200	Weak transcription	Osteobl	bone
10	chr7:27068800-27071800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr7:27069200-27070400	Weak transcription	Fetal Kidney	kidney
12	chr7:27069200-27070600	Weak transcription	Stomach Mucosa	stomach
13	chr7:27069400-27069800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:27069400-27070000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr7:27069600-27071200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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