Variant report

Variant	rs846559
Chromosome Location	chr1:210234236-210234237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210225380..210227354-chr1:210231385..210234453,3	K562	blood:
2	chr1:210191948..210194916-chr1:210232522..210235373,2	K562	blood:

Variant related genes	Relation type
ENSG00000143469	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1028325	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1040423	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10746423	0.87[EUR][1000 genomes]
rs10779516	0.90[EUR][1000 genomes]
rs10779517	0.91[EUR][1000 genomes]
rs10779518	0.91[EUR][1000 genomes]
rs10779523	0.85[EUR][1000 genomes]
rs10863799	0.89[EUR][1000 genomes]
rs10863811	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1099863	0.93[EUR][1000 genomes]
rs11119363	0.85[EUR][1000 genomes]
rs11119369	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11119370	0.83[EUR][1000 genomes]
rs11119374	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11119375	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119376	0.90[EUR][1000 genomes]
rs11119378	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11119382	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11119407	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119409	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11119413	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11119414	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12025114	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12042135	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12079815	0.81[EUR][1000 genomes]
rs12083466	0.84[EUR][1000 genomes]
rs12092530	0.85[EUR][1000 genomes]
rs126277	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs126278	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1334567	0.89[EUR][1000 genomes]
rs1334568	0.89[EUR][1000 genomes]
rs1334569	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1387933	0.92[EUR][1000 genomes]
rs1387934	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490419	0.84[EUR][1000 genomes]
rs170552	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs170553	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170555	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs170557	0.93[EUR][1000 genomes]
rs170558	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183450	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189000	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189001	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2046849	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2142861	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2200970	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2205987	0.86[EUR][1000 genomes]
rs2205988	0.89[EUR][1000 genomes]
rs2205989	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs227168	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227169	0.93[EUR][1000 genomes]
rs227170	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs227171	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227172	0.93[EUR][1000 genomes]
rs227173	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227174	0.93[EUR][1000 genomes]
rs227175	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227176	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227177	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227179	0.92[EUR][1000 genomes]
rs227181	0.93[EUR][1000 genomes]
rs227182	0.93[EUR][1000 genomes]
rs227183	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227184	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227186	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227187	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227188	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227189	0.88[EUR][1000 genomes]
rs227190	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs227191	0.93[EUR][1000 genomes]
rs227193	0.93[EUR][1000 genomes]
rs227195	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227196	0.93[EUR][1000 genomes]
rs227197	0.93[EUR][1000 genomes]
rs227200	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227201	0.93[EUR][1000 genomes]
rs227202	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227203	0.93[EUR][1000 genomes]
rs227204	0.94[EUR][1000 genomes]
rs227205	0.94[EUR][1000 genomes]
rs227206	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227207	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227209	0.93[EUR][1000 genomes]
rs227211	0.93[EUR][1000 genomes]
rs227216	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227217	0.91[EUR][1000 genomes]
rs227218	0.92[EUR][1000 genomes]
rs227219	0.92[EUR][1000 genomes]
rs227221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227223	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs227224	0.93[EUR][1000 genomes]
rs227225	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227226	0.90[EUR][1000 genomes]
rs227227	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227228	0.93[EUR][1000 genomes]
rs227229	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227230	0.93[EUR][1000 genomes]
rs227232	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357212	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2473073	0.89[EUR][1000 genomes]
rs2636373	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636376	0.93[EUR][1000 genomes]
rs2743889	0.93[EUR][1000 genomes]
rs2743891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34946555	0.86[EUR][1000 genomes]
rs4454550	0.88[EUR][1000 genomes]
rs4462143	0.88[EUR][1000 genomes]
rs4844947	0.88[EUR][1000 genomes]
rs4844948	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6540568	0.90[EUR][1000 genomes]
rs6540569	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs6540570	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs6540573	0.91[EUR][1000 genomes]
rs6540580	0.89[EUR][1000 genomes]
rs6656855	0.89[EUR][1000 genomes]
rs6657984	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6662445	0.90[EUR][1000 genomes]
rs6667057	0.88[EUR][1000 genomes]
rs6678081	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682334	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682546	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6689456	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702257	0.88[EUR][1000 genomes]
rs6702961	0.88[EUR][1000 genomes]
rs701947	0.96[CEU][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs701948	0.96[CEU][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs724054	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7513171	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514257	0.93[EUR][1000 genomes]
rs7517019	0.83[EUR][1000 genomes]
rs7519750	0.89[EUR][1000 genomes]
rs7525980	0.93[EUR][1000 genomes]
rs7528647	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7530426	0.91[EUR][1000 genomes]
rs7544033	0.84[EUR][1000 genomes]
rs7547709	0.93[EUR][1000 genomes]
rs7548989	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7549523	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7549696	0.85[EUR][1000 genomes]
rs846545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs846546	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs846548	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs846549	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs846550	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs846551	0.93[EUR][1000 genomes]
rs846552	0.93[EUR][1000 genomes]
rs846553	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs846554	0.93[EUR][1000 genomes]
rs846555	0.93[EUR][1000 genomes]
rs846556	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846557	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860155	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9429827	0.88[EUR][1000 genomes]
rs9429829	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9429830	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9430020	0.81[EUR][1000 genomes]
rs9430024	0.85[EUR][1000 genomes]
rs9430026	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9659395	0.89[EUR][1000 genomes]
rs9662387	0.83[EUR][1000 genomes]
rs986057	0.96[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873141	chr1:210228131-210296910	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv873142	chr1:210233610-210291121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv873143	chr1:210233610-210296910	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs846559	CR1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210221400-210243200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:210223600-210245600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:210224400-210250000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:210232200-210235200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:210234200-210234400	Enhancers	Pancreatic Islets	Pancreatic Islet

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