Variant report

Variant	rs6898399
Chromosome Location	chr5:95289398-95289399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95287964..95290450-chr5:95291198..95293883,2	MCF-7	breast:
2	chr5:95282858..95287226-chr5:95287357..95291460,4	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10052503	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073752	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10515232	0.93[EUR][1000 genomes]
rs11738945	0.80[EUR][1000 genomes]
rs11742959	0.80[EUR][1000 genomes]
rs12055262	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085333	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1862313	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2112566	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2161318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546199	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734131	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756703	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777162	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777163	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777164	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3777165	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777166	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777167	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3777168	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777171	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777173	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777175	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777178	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777179	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822750	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563648	0.83[ASN][1000 genomes]
rs55841351	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56002885	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57243277	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57595413	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921760	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59307279	0.93[EUR][1000 genomes]
rs6556894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861531	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6877821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881355	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881872	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883880	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6894651	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897997	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6898371	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72656689	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7700895	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705279	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705720	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7724599	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889302	0.85[ASN][1000 genomes]
rs918629	0.83[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
rs6898399	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr5:95272800-95291200	Weak transcription	NH-A	brain
5	chr5:95273000-95291200	Weak transcription	HSMMtube	muscle
6	chr5:95274800-95292200	Weak transcription	Placenta	Placenta
7	chr5:95275400-95291400	Weak transcription	NHDF-Ad	bronchial
8	chr5:95277000-95290800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:95277200-95291600	Weak transcription	Ovary	ovary
10	chr5:95277800-95291600	Weak transcription	Fetal Intestine Large	intestine
11	chr5:95278000-95292200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:95281000-95290800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:95281000-95291600	Weak transcription	Aorta	Aorta
14	chr5:95281000-95291600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:95281000-95294000	Weak transcription	Esophagus	oesophagus
16	chr5:95282000-95290600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr5:95282200-95290400	Weak transcription	Left Ventricle	heart
18	chr5:95282400-95290400	Weak transcription	Right Atrium	heart
19	chr5:95282400-95291000	Weak transcription	Adipose Nuclei	Adipose
20	chr5:95282400-95291200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:95282400-95294000	Weak transcription	Pancreas	Pancrea
22	chr5:95282600-95290800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:95282600-95294000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:95282800-95290600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:95284000-95290800	Weak transcription	Small Intestine	intestine
26	chr5:95284600-95295200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:95284800-95292000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:95285800-95290600	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:95286000-95290600	Weak transcription	Stomach Mucosa	stomach
30	chr5:95286000-95293800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:95286200-95290400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:95286200-95290800	Weak transcription	Fetal Heart	heart
33	chr5:95286400-95290800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr5:95286400-95291600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:95286400-95295200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:95287000-95294800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:95287200-95289600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:95287400-95289600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:95287400-95289600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:95287400-95289600	Genic enhancers	HepG2	liver
41	chr5:95287400-95289600	Strong transcription	HSMM	muscle
42	chr5:95287600-95289400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:95287600-95291200	Weak transcription	Psoas Muscle	Psoas
44	chr5:95287600-95291800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:95288000-95291600	Weak transcription	Primary B cells from cord blood	blood
46	chr5:95288000-95294400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:95288200-95290400	Weak transcription	NHLF	lung
48	chr5:95288400-95289400	Enhancers	Brain Substantia Nigra	brain
49	chr5:95288400-95290800	Genic enhancers	Hela-S3	cervix
50	chr5:95288600-95289400	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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