Variant report

Variant	rs56261855
Chromosome Location	chr2:128276474-128276475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128271646..128276478-chr2:128281725..128284912,6	MCF-7	breast:
2	chr2:128266970..128268889-chr2:128276215..128277935,2	K562	blood:
3	chr2:128261896..128263510-chr2:128274166..128276871,2	K562	blood:
4	chr2:128271568..128276709-chr2:128278536..128286742,13	K562	blood:
5	chr2:128275312..128279572-chr2:128410107..128412898,3	K562	blood:
6	chr2:128258277..128260022-chr2:128274058..128277038,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10496663	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10928769	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11681225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682864	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11685630	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11690086	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12053309	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12233101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12616100	0.84[ASN][1000 genomes]
rs12616200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618494	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12619773	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12620037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015274	0.95[AFR][1000 genomes]
rs17015334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015401	0.83[ASN][1000 genomes]
rs1864553	0.85[ASN][1000 genomes]
rs2082182	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099209	0.84[ASN][1000 genomes]
rs2288655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35208523	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732205	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3889307	0.84[EUR][1000 genomes]
rs55688542	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56100618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56327685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62156572	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62156576	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62156599	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6758364	0.84[ASN][1000 genomes]
rs72843327	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586672	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs777556	0.97[ASN][1000 genomes]
rs873099	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs56261855	AC068282.3	cis	Esophagus Muscularis	GTEx
rs56261855	AC068282.3	cis	Esophagus Mucosa	GTEx
rs56261855	AC068282.3	cis	Whole Blood	GTEx
rs56261855	AC068282.3	cis	Thyroid	GTEx
rs56261855	AC068282.3	cis	Artery Tibial	GTEx
rs56261855	AC068282.3	cis	Muscle Skeletal	GTEx
rs56261855	AC068282.3	cis	lung	GTEx
rs56261855	AC068282.3	cis	Nerve Tibial	GTEx
rs56261855	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs56261855	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128262600-128283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:128263000-128281200	Weak transcription	Fetal Kidney	kidney
3	chr2:128263200-128282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128266000-128282800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:128267200-128282000	Weak transcription	Fetal Brain Male	brain
6	chr2:128267600-128281200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:128267600-128282000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:128268400-128281600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:128268600-128281600	Strong transcription	Fetal Thymus	thymus
10	chr2:128270200-128282600	Weak transcription	Small Intestine	intestine
11	chr2:128270400-128276600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:128271000-128278600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:128271400-128281400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:128271400-128281800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:128271400-128281800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr2:128271600-128279000	Strong transcription	Liver	Liver
17	chr2:128271800-128281400	Strong transcription	Fetal Intestine Large	intestine
18	chr2:128272000-128281200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:128272400-128282800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:128272400-128282800	Weak transcription	Colonic Mucosa	Colon
21	chr2:128272600-128280600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:128272600-128281000	Strong transcription	HepG2	liver
23	chr2:128272800-128282800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:128273400-128278600	Strong transcription	Fetal Lung	lung
25	chr2:128273600-128277400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:128273600-128281200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:128273600-128281200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:128273600-128281400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:128273600-128281600	Strong transcription	Primary B cells from cord blood	blood
30	chr2:128273600-128281800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:128273600-128281800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:128273600-128282800	Weak transcription	Gastric	stomach
33	chr2:128273800-128277600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:128273800-128279400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:128273800-128279600	Weak transcription	Esophagus	oesophagus
36	chr2:128273800-128281600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:128273800-128281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:128274000-128278000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:128274000-128281600	Weak transcription	Fetal Heart	heart
40	chr2:128274000-128281800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:128274000-128282200	Weak transcription	Pancreas	Pancrea
42	chr2:128274200-128277800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:128274200-128280600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:128274200-128281200	Weak transcription	Brain Angular Gyrus	brain
45	chr2:128274200-128281400	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:128274200-128281600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:128274200-128281800	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:128274200-128281800	Strong transcription	K562	blood
49	chr2:128274200-128282000	Strong transcription	Placenta	Placenta
50	chr2:128274200-128282200	Weak transcription	Lung	lung

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