Variant report

Variant	rs1862313
Chromosome Location	chr5:95272357-95272358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:94982546..94984387-chr5:95271900..95273810,2	K562	blood:
2	chr5:95270893..95273620-chr5:95274883..95277276,2	MCF-7	breast:
3	chr5:95271606..95274908-chr5:95279196..95282633,3	K562	blood:

Variant related genes	Relation type
ENSG00000175449	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10052503	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10073752	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10515232	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11738945	0.84[EUR][1000 genomes]
rs11742959	0.84[EUR][1000 genomes]
rs12055262	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17085333	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112566	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161318	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546199	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3734131	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756703	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777162	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777163	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777165	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777166	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777167	0.81[EUR][1000 genomes]
rs3777168	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777171	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777173	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777175	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777178	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777179	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777182	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3777183	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3777190	0.82[AFR][1000 genomes]
rs3777192	0.82[AFR][1000 genomes]
rs3822750	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55841351	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56002885	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57243277	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57595413	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58921760	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59307279	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6556894	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556898	0.83[ASN][1000 genomes]
rs6861531	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877821	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6881355	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881872	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883880	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894651	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6897997	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898371	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6898399	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72656689	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7700895	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7705279	0.92[EUR][1000 genomes]
rs7705720	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7710422	0.87[ASN][1000 genomes]
rs7724599	0.92[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	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1862313	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
3	chr5:95243400-95278800	Weak transcription	Lung	lung
4	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:95252200-95272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:95253800-95272400	Weak transcription	Placenta	Placenta
7	chr5:95257400-95276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:95259400-95273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:95259400-95274600	Weak transcription	Psoas Muscle	Psoas
10	chr5:95260000-95280600	Weak transcription	Esophagus	oesophagus
11	chr5:95260800-95273400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
13	chr5:95262200-95272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:95263800-95278400	Weak transcription	Colonic Mucosa	Colon
16	chr5:95264800-95272400	Weak transcription	Stomach Mucosa	stomach
17	chr5:95264800-95275200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:95264800-95276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:95264800-95279800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr5:95264800-95285600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:95265000-95285600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:95265400-95281800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:95266600-95274400	Weak transcription	NHLF	lung
25	chr5:95267000-95272600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:95267000-95277000	Weak transcription	Fetal Thymus	thymus
27	chr5:95267200-95280200	Weak transcription	Aorta	Aorta
28	chr5:95267400-95280000	Weak transcription	A549	lung
29	chr5:95267600-95274800	Weak transcription	NHDF-Ad	bronchial
30	chr5:95268400-95274600	Weak transcription	Brain Anterior Caudate	brain
31	chr5:95269600-95273000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:95269800-95275000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:95270000-95274200	Genic enhancers	Osteobl	bone
34	chr5:95270000-95283200	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr5:95270200-95273600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:95270400-95272400	Weak transcription	Brain Hippocampus Middle	brain
37	chr5:95270400-95272600	Weak transcription	Brain Substantia Nigra	brain
38	chr5:95270400-95276600	Weak transcription	Ovary	ovary
39	chr5:95270400-95276600	Weak transcription	Small Intestine	intestine
40	chr5:95270400-95277000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:95270400-95277400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr5:95270400-95284800	Weak transcription	Fetal Intestine Small	intestine
43	chr5:95270400-95285400	Weak transcription	Right Ventricle	heart
44	chr5:95270600-95272800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:95270600-95276600	Weak transcription	Fetal Heart	heart
46	chr5:95270800-95279200	Genic enhancers	HepG2	liver
47	chr5:95271200-95272400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr5:95271200-95272600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:95271200-95273200	Genic enhancers	Liver	Liver
50	chr5:95271200-95273800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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