Variant report

Variant	rs6894651
Chromosome Location	chr5:95292267-95292268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95287964..95290450-chr5:95291198..95293883,2	MCF-7	breast:
2	chr5:95290720..95292319-chr5:96270135..96272344,2	MCF-7	breast:
3	chr5:95204164..95206155-chr5:95291916..95293467,2	K562	blood:
4	chr5:95289886..95294659-chr5:95295662..95298234,5	MCF-7	breast:
5	chr5:95285461..95287509-chr5:95291864..95293445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000251314	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10052503	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073752	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10515232	0.94[EUR][1000 genomes]
rs12055262	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085333	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1862313	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2112566	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2161318	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546199	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734131	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756703	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777162	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777164	0.84[EUR][1000 genomes]
rs3777165	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777166	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777167	0.83[EUR][1000 genomes]
rs3777168	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777171	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777173	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777175	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777178	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777179	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822750	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563648	0.83[ASN][1000 genomes]
rs55841351	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56002885	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243277	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57595413	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921760	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59307279	0.92[EUR][1000 genomes]
rs6556894	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861531	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6877821	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881355	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881872	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883880	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6897997	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6898371	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898399	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72656689	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700895	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705279	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705720	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7710422	0.80[EUR][1000 genomes]
rs7724599	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889302	0.85[ASN][1000 genomes]
rs918629	0.84[EUR][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	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
2	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
3	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
rs6894651	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95260800-95295200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:95262200-95295400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:95264800-95293800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:95281000-95294000	Weak transcription	Esophagus	oesophagus
5	chr5:95282400-95294000	Weak transcription	Pancreas	Pancrea
6	chr5:95282600-95294000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:95284600-95295200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:95286000-95293800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:95286400-95295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:95287000-95294800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:95288000-95294400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:95288600-95292800	Enhancers	Fetal Brain Male	brain
13	chr5:95289200-95294000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:95290400-95293000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:95290400-95294000	Active TSS	Right Ventricle	heart
16	chr5:95290600-95292600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:95290600-95293000	Enhancers	Colon Smooth Muscle	Colon
18	chr5:95290600-95293600	Enhancers	Brain Substantia Nigra	brain
19	chr5:95290600-95293800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:95290600-95294000	Enhancers	Stomach Mucosa	stomach
21	chr5:95290600-95296800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
22	chr5:95290800-95292400	Enhancers	Fetal Stomach	stomach
23	chr5:95290800-95292800	Enhancers	HUVEC	blood vessel
24	chr5:95290800-95293000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr5:95290800-95295000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:95291000-95292800	Enhancers	Adipose Nuclei	Adipose
27	chr5:95291000-95293800	Enhancers	Brain Angular Gyrus	brain
28	chr5:95291200-95292400	Transcr. at gene 5' and 3'	NHEK	skin
29	chr5:95291200-95292600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr5:95291200-95293000	Enhancers	NH-A	brain
31	chr5:95291200-95296000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr5:95291400-95292400	Transcr. at gene 5' and 3'	HepG2	liver
33	chr5:95291400-95292600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:95291400-95292800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:95291400-95292800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:95291400-95292800	Active TSS	Fetal Brain Female	brain
37	chr5:95291400-95293800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:95291400-95293800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr5:95291400-95294000	Enhancers	NHDF-Ad	bronchial
40	chr5:95291400-95296200	Transcr. at gene 5' and 3'	HMEC	breast
41	chr5:95291600-95292400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:95291600-95292400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr5:95291600-95292400	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr5:95291600-95292400	Enhancers	Fetal Intestine Large	intestine
45	chr5:95291600-95292600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:95291600-95292800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:95291600-95292800	Enhancers	Fetal Intestine Small	intestine
48	chr5:95291600-95292800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr5:95291600-95292800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr5:95291800-95292400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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