Variant report

Variant	rs4916402
Chromosome Location	chr1:171815948-171815949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171809949..171812154-chr1:171814314..171816652,2	K562	blood:
2	chr1:171815099..171817651-chr1:171819737..171821446,2	K562	blood:
3	chr1:171810327..171813240-chr1:171815906..171818377,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197959	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1022541	0.85[ASN][1000 genomes]
rs1040517	0.85[ASN][1000 genomes]
rs10737338	0.86[ASN][1000 genomes]
rs10753202	0.85[ASN][1000 genomes]
rs10753203	0.83[ASN][1000 genomes]
rs10753204	0.85[ASN][1000 genomes]
rs10753205	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1076700	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798695	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798701	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798702	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798705	0.86[ASN][1000 genomes]
rs10798706	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798716	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798722	0.85[ASN][1000 genomes]
rs10798725	0.85[ASN][1000 genomes]
rs10798726	0.85[ASN][1000 genomes]
rs10913908	0.85[ASN][1000 genomes]
rs1118173	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11808234	0.84[AMR][1000 genomes]
rs12021814	0.83[ASN][1000 genomes]
rs12239702	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12405583	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535301	0.83[ASN][1000 genomes]
rs1555100	0.83[ASN][1000 genomes]
rs1972340	0.82[ASN][1000 genomes]
rs1980488	0.85[ASN][1000 genomes]
rs2206543	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235696	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421915	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421947	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2901600	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4500358	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916235	0.86[ASN][1000 genomes]
rs4916400	0.86[ASN][1000 genomes]
rs4916401	0.86[ASN][1000 genomes]
rs4916403	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916404	0.85[ASN][1000 genomes]
rs6425454	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425455	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425456	0.86[ASN][1000 genomes]
rs6425468	0.85[ASN][1000 genomes]
rs6657315	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660011	0.85[ASN][1000 genomes]
rs6665335	0.86[ASN][1000 genomes]
rs6679341	0.85[ASN][1000 genomes]
rs6683945	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6685974	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686260	0.83[ASN][1000 genomes]
rs6690848	0.83[ASN][1000 genomes]
rs6701033	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6702944	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71523161	0.83[ASN][1000 genomes]
rs742509	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742510	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514627	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517331	0.86[ASN][1000 genomes]
rs7526653	0.86[ASN][1000 genomes]
rs7554700	0.85[ASN][1000 genomes]
rs7554935	0.85[ASN][1000 genomes]
rs926545	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926546	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965051	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171812200-171816600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:171812200-171833200	Weak transcription	Brain Germinal Matrix	brain
3	chr1:171812400-171817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:171812400-171819200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:171813800-171816400	Weak transcription	Brain Anterior Caudate	brain
6	chr1:171814000-171820000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:171814200-171816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:171814200-171816200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:171814400-171817200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:171814600-171816000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:171814600-171816000	Weak transcription	Fetal Brain Male	brain
12	chr1:171814600-171833400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:171815600-171818400	Enhancers	Brain Angular Gyrus	brain
14	chr1:171815800-171818600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:171815800-171820200	Enhancers	Brain Inferior Temporal Lobe	brain

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