Variant report

Variant	rs10421280
Chromosome Location	chr19:19973452-19973453
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	chr19:19971677..19974532-chr19:19975356..19978312,2	MCF-7	breast:
2	chr19:19970667..19974781-chr19:19975210..19979739,6	K562	blood:

Variant related genes	Relation type
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008112	0.86[CHB][hapmap]
rs10403255	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10407726	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10412710	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10414919	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1048421	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs12327878	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610390	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13344370	0.88[GIH][hapmap];0.88[JPT][hapmap]
rs1469700	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469701	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469702	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060239	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2110589	0.86[CHB][hapmap]
rs2304169	0.83[AFR][1000 genomes]
rs2335368	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs28590063	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3926422	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808221	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809002	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809003	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809015	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs6511058	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs66624169	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246569	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap]
rs7250258	0.82[AFR][1000 genomes]
rs7252427	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256224	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs7260247	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105482	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8113576	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs8113694	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10421280	ZNF493	cis	parietal	SCAN
rs10421280	ATP13A1	cis	parietal	SCAN
rs10421280	ZNF253	cis	Nerve Tibial	GTEx
rs10421280	ZNF682	cis	Muscle Skeletal	GTEx
rs10421280	ZNF506	cis	cerebellum	SCAN
rs10421280	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs10421280	ZNF93	cis	cerebellum	SCAN
rs10421280	ZNF253	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19972000-19976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr19:19972000-19976000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr19:19972000-19976000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:19972000-19976000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:19972000-19976000	Weak transcription	Right Ventricle	heart
6	chr19:19972000-19976600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:19972200-19976000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:19972200-19976000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:19972200-19976000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:19972200-19976000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:19972200-19976000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:19972200-19976000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:19972200-19976000	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:19972200-19976000	Weak transcription	Pancreas	Pancrea
15	chr19:19972200-19976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:19972200-19976600	Weak transcription	Spleen	Spleen
17	chr19:19972400-19976000	Weak transcription	Placenta	Placenta
18	chr19:19973400-19973800	Enhancers	HepG2	liver

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