Variant report

Variant	rs4655690
Chromosome Location	chr1:67659896-67659897
allele	A/G
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	chr1:67658627-67660266	K562	blood:	n/a	n/a
2	CHD2	chr1:67659580-67660575	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67658711..67660286-chr1:67661599..67664235,2	K562	blood:

Variant related genes	Relation type
RNU6-586P	TF binding region
ENSG00000253074	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10127763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10889665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889668	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11801083	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321156	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs1358748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358749	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884443	0.94[EUR][1000 genomes]
rs2064691	0.90[EUR][1000 genomes]
rs2180296	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2863203	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4655521	0.86[EUR][1000 genomes]
rs4655522	0.86[EUR][1000 genomes]
rs4655681	0.95[EUR][1000 genomes]
rs4655688	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6666144	0.90[EUR][1000 genomes]
rs6683455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684024	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687620	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703475	0.90[EUR][1000 genomes]
rs7518757	0.85[EUR][1000 genomes]
rs7540900	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4655690	IL23R	cis	parietal	SCAN
rs4655690	WLS	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67656000-67661200	Weak transcription	Small Intestine	intestine
2	chr1:67656000-67663400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:67656800-67661400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:67656800-67661400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:67657400-67661800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:67658000-67661400	Enhancers	GM12878-XiMat	blood
7	chr1:67658200-67660400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:67658400-67661400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:67658600-67661600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:67658800-67660000	Enhancers	K562	blood
11	chr1:67659000-67660000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:67659200-67662000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:67659400-67660200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:67659400-67661400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:67659400-67661400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:67659400-67661800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:67659400-67662000	Enhancers	Primary T cells from cord blood	blood
18	chr1:67659400-67662800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:67659800-67660200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:67659800-67660400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:67659800-67661000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:67659800-67661200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:67659800-67661200	Enhancers	Fetal Thymus	thymus

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