Variant report

Variant	rs56401468
Chromosome Location	chr2:180857757-180857758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180856151..180858143-chr2:180858684..180861516,4	K562	blood:
2	chr2:180853987..180858139-chr2:180866524..180870001,3	MCF-7	breast:
3	chr2:180856164..180859331-chr2:180861905..180864411,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12465592	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12468986	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12693214	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12693215	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16867131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1904850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2367990	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs259810	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259811	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2678936	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3843323	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3845701	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856415	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433816	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433818	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6433820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433821	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6722147	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6727890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6733426	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6744281	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6759271	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72958863	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72960660	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72960664	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72960701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72962517	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72962575	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs818661	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9288045	0.84[AMR][1000 genomes];0.87[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	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1006598	chr2:180766983-180923051	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv531444	chr2:180796233-181434590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180807000-180858400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:180808200-180860400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:180809400-180871000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:180813400-180868200	Weak transcription	Stomach Mucosa	stomach
5	chr2:180816800-180860400	Weak transcription	Right Ventricle	heart
6	chr2:180816800-180868400	Weak transcription	Pancreas	Pancrea
7	chr2:180816800-180869000	Weak transcription	Spleen	Spleen
8	chr2:180816800-180870600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:180817200-180860400	Weak transcription	Aorta	Aorta
10	chr2:180817200-180860400	Weak transcription	Gastric	stomach
11	chr2:180819000-180871000	Weak transcription	Esophagus	oesophagus
12	chr2:180821600-180858800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:180822200-180858200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:180823400-180870600	Weak transcription	Fetal Intestine Small	intestine
15	chr2:180829600-180871200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:180830800-180871000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:180831000-180860400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:180832800-180860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:180834200-180858200	Strong transcription	Primary B cells from cord blood	blood
20	chr2:180836800-180870400	Weak transcription	A549	lung
21	chr2:180839800-180870400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:180840600-180858200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:180840600-180858200	Strong transcription	Dnd41	blood
24	chr2:180841000-180858200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:180843000-180870200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:180846800-180867000	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:180846800-180869800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:180847600-180866200	Weak transcription	Psoas Muscle	Psoas
29	chr2:180848400-180858200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:180849000-180858200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:180849000-180869600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:180850400-180862200	Weak transcription	Small Intestine	intestine
33	chr2:180850600-180870800	Weak transcription	HSMMtube	muscle
34	chr2:180851000-180870200	Weak transcription	Hela-S3	cervix
35	chr2:180851600-180870400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:180851800-180870400	Weak transcription	HUVEC	blood vessel
37	chr2:180852000-180859200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:180852000-180860600	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:180852000-180865000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:180852200-180870600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:180852400-180860400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:180853200-180868000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:180853600-180869600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:180854800-180858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:180855000-180858200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:180855000-180858200	Strong transcription	Liver	Liver
47	chr2:180855000-180858400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:180855000-180858600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:180855200-180858000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:180855200-180858000	Strong transcription	Primary B cells from peripheral blood	blood

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