Variant report

Variant	rs4808221
Chromosome Location	chr19:19972215-19972216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19971500-19972353	H1-hESC	embryonic stem cell:	n/a	n/a
2	GTF2F1	chr19:19971757-19972320	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF7	chr19:19971513-19972289	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:19971482-19972245	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr19:19971851-19972230	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr19:19971347-19972232	H1-hESC	embryonic stem cell:	n/a	chr19:19971601-19971610 chr19:19971596-19971615
7	SP1	chr19:19971852-19972317	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr19:19971485-19972235	H1-hESC	embryonic stem cell:	n/a	chr19:19971708-19971718
9	CHD1	chr19:19971545-19972273	H1-hESC	embryonic stem cell:	n/a	chr19:19972107-19972117
10	POLR2A	chr19:19971317-19972366	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr19:19971442-19972322	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr19:19971571-19972282	H1-hESC	embryonic stem cell:	n/a	chr19:19971708-19971718
13	NFYB	chr19:19971885-19972235	K562	blood:	n/a	chr19:19972088-19972098 chr19:19972086-19972100 chr19:19972087-19972100 chr19:19972057-19972071
14	SIN3A	chr19:19971435-19972221	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr19:19971623-19972263	H1-hESC	embryonic stem cell:	n/a	chr19:19972015-19972025 chr19:19972016-19972024 chr19:19972017-19972024 chr19:19972016-19972024
16	POLR2A	chr19:19971313-19972449	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:19971382-19972323	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr19:19971524-19972347	H1-hESC	embryonic stem cell:	n/a	n/a
19	CHD2	chr19:19971750-19972238	H1-hESC	embryonic stem cell:	n/a	chr19:19972107-19972117
20	TAF1	chr19:19971290-19972331	H1-hESC	embryonic stem cell:	n/a	n/a
21	REST	chr19:19971775-19972289	H1-hESC	embryonic stem cell:	n/a	n/a
22	SP1	chr19:19971697-19972287	H1-hESC	embryonic stem cell:	n/a	n/a

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
ZNF253	TF binding region
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1008112	0.83[CHB][hapmap]
rs10403255	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10407726	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10412710	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10414919	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs10421280	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]
rs1048421	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs12327878	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610390	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13344370	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1469700	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469701	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469702	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2060239	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2110589	0.82[CHB][hapmap]
rs2304169	0.87[AFR][1000 genomes]
rs2335368	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs28590063	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3926422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4809002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4809003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809015	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs6511058	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs66624169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246569	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs7250258	0.86[AFR][1000 genomes]
rs7252427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256224	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs7260247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105482	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs8113576	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs8113694	0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4808221	ZNF682	cis	Muscle Skeletal	GTEx
rs4808221	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs4808221	ZNF253	cis	Nerve Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19971000-19972400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:19971400-19972400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:19971600-19972800	Enhancers	HepG2	liver
4	chr19:19972000-19976000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:19972000-19976000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr19:19972000-19976000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:19972000-19976000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:19972000-19976000	Weak transcription	Right Ventricle	heart
9	chr19:19972000-19976600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:19972200-19976000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr19:19972200-19976000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:19972200-19976000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr19:19972200-19976000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:19972200-19976000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:19972200-19976000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:19972200-19976000	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:19972200-19976000	Weak transcription	Pancreas	Pancrea
18	chr19:19972200-19976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:19972200-19976600	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links