Variant report

Variant	rs450953
Chromosome Location	chr1:86212324-86212325
allele	C/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	CTCF	chr1:86212320-86212470	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86045430..86047894-chr1:86210849..86213430,2	K562	blood:
2	chr1:86211855..86213533-chr1:86285001..86287776,2	K562	blood:

Variant related genes	Relation type
COL24A1	TF binding region
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10747324	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873711	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10873718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094360	0.87[EUR][1000 genomes]
rs12037294	0.80[EUR][1000 genomes]
rs12756841	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758966	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1360239	0.80[EUR][1000 genomes]
rs1481200	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1764287	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes]
rs1764294	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1764295	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs1764296	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1764298	0.81[ASN][1000 genomes]
rs1775985	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs1775986	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs1775987	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[EUR][1000 genomes]
rs1775991	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1775992	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs1813656	0.82[AFR][1000 genomes]
rs2014733	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2014750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026772	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs2389973	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2389974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2389975	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764470	0.87[AMR][1000 genomes]
rs2970548	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs369999	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs381453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383558	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399547	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs401657	0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425357	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs429040	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs430956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379699	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs438401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444875	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4949917	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs4949918	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs550329	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6576789	0.84[AFR][1000 genomes]
rs6673975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686719	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6694808	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs7521240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7528385	1.00[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7529942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533395	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs7535884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544908	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7547023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821378	0.87[YRI][hapmap]
rs821380	0.84[YRI][hapmap]
rs821383	0.96[EUR][1000 genomes]
rs821385	0.81[EUR][1000 genomes]
rs821387	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes]
rs821388	0.80[YRI][hapmap];0.96[EUR][1000 genomes]
rs821390	0.87[YRI][hapmap]
rs821397	0.87[EUR][1000 genomes]
rs821400	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[EUR][1000 genomes]
rs821402	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs821403	0.84[YRI][hapmap]
rs849158	0.96[EUR][1000 genomes]
rs9324152	0.87[YRI][hapmap]
rs9324153	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9651138	0.88[EUR][1000 genomes]
rs9661608	1.00[CEU][hapmap];0.84[YRI][hapmap];0.87[EUR][1000 genomes]
rs9661951	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs9701898	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[EUR][1000 genomes]
rs9793556	1.00[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3344445	chr1:86212214-86221212	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86207800-86221800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:86210200-86213600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86210800-86220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:86211400-86220400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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