Variant report

Variant	rs56124923
Chromosome Location	chr1:173824970-173824971
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173823430..173826161-chr1:173990406..173993214,2	MCF-7	breast:
2	chr1:173791743..173795924-chr1:173822974..173827118,6	K562	blood:
3	chr1:173808404..173810597-chr1:173824341..173827364,3	MCF-7	breast:
4	chr1:173793044..173798309-chr1:173822396..173826299,5	K562	blood:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10081990	0.88[AMR][1000 genomes]
rs10158663	0.88[AMR][1000 genomes]
rs10798298	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912677	0.88[AMR][1000 genomes]
rs10912678	0.88[AMR][1000 genomes]
rs10912680	0.88[AMR][1000 genomes]
rs10912682	0.88[AMR][1000 genomes]
rs10912684	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1115487	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070556	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12082206	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12085748	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12085894	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094130	0.88[AMR][1000 genomes]
rs12095090	0.88[AMR][1000 genomes]
rs12096832	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322771	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1322772	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1474907	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846383	0.88[AMR][1000 genomes]
rs16846420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2224657	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578576	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59845733	0.88[AMR][1000 genomes]
rs6425257	0.88[AMR][1000 genomes]
rs6663880	0.88[AMR][1000 genomes]
rs6675762	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6686455	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689764	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691327	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691922	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6692452	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6695782	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6698348	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6702485	0.88[AMR][1000 genomes]
rs7518130	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7522788	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7534521	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536773	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7552840	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9282959	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9282960	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286886	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286887	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286890	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9286894	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425415	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425418	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425419	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425420	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425421	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425422	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425423	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425424	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425425	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425426	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425734	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425736	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425738	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425740	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425741	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425742	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9425746	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9425747	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425750	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425751	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425752	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425758	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425759	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425761	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9425774	0.83[AMR][1000 genomes]
rs9442660	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970488	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970633	0.88[AMR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
6	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
8	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:173801200-173825000	Weak transcription	Brain Angular Gyrus	brain
12	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:173809200-173825200	Weak transcription	NHDF-Ad	bronchial
14	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
15	chr1:173811000-173825000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:173811200-173825000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
19	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
20	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:173813600-173825400	Weak transcription	Brain Anterior Caudate	brain
22	chr1:173814600-173826400	Weak transcription	Hela-S3	cervix
23	chr1:173815000-173826000	Weak transcription	Esophagus	oesophagus
24	chr1:173816000-173825000	Weak transcription	Spleen	Spleen
25	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
26	chr1:173818400-173829000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:173818400-173829800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:173818600-173825200	Strong transcription	Fetal Stomach	stomach
29	chr1:173818600-173829600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:173818600-173830200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:173818800-173827200	Strong transcription	Primary T cells from cord blood	blood
34	chr1:173818800-173827800	Strong transcription	Dnd41	blood
35	chr1:173819200-173828200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:173819200-173834000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:173819400-173827600	Strong transcription	HMEC	breast
40	chr1:173819400-173829800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:173819400-173832000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:173819600-173830000	Weak transcription	Right Atrium	heart
44	chr1:173819600-173834000	Strong transcription	Fetal Thymus	thymus
45	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:173819800-173825600	Strong transcription	Ovary	ovary
47	chr1:173819800-173827600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr1:173820400-173828200	Strong transcription	Adipose Nuclei	Adipose
49	chr1:173820400-173828600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:173820600-173827400	Strong transcription	HSMM	muscle

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