Variant report

Variant	rs2279825
Chromosome Location	chr2:98611833-98611834
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	chr2:98523325..98524831-chr2:98610615..98613167,2	MCF-7	breast:
2	chr2:98610350..98614892-chr2:98700211..98704879,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168658	Chromatin interaction
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10176201	0.83[ASN][1000 genomes]
rs10182941	0.85[ASN][1000 genomes]
rs10200949	0.85[ASN][1000 genomes]
rs10211231	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1071885	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865055	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123949	0.83[ASN][1000 genomes]
rs11123966	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11690482	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11693874	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888323	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11899171	0.80[ASN][1000 genomes]
rs12712174	0.84[ASN][1000 genomes]
rs13003978	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13006817	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13022778	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1317178	0.85[ASN][1000 genomes]
rs13405546	0.85[ASN][1000 genomes]
rs1466924	0.85[ASN][1000 genomes]
rs1503200	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1922280	0.85[ASN][1000 genomes]
rs1922282	0.85[ASN][1000 genomes]
rs2017028	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141862	0.85[ASN][1000 genomes]
rs2279826	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309316	0.85[ASN][1000 genomes]
rs2309356	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088327	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560167	0.83[ASN][1000 genomes]
rs6543161	0.83[ASN][1000 genomes]
rs6543177	0.83[ASN][1000 genomes]
rs6543202	0.85[ASN][1000 genomes]
rs6543210	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6709571	0.83[ASN][1000 genomes]
rs6719556	0.81[ASN][1000 genomes]
rs6723466	0.85[ASN][1000 genomes]
rs6723653	0.86[ASN][1000 genomes]
rs6744331	0.83[ASN][1000 genomes]
rs7561104	0.83[ASN][1000 genomes]
rs7562695	0.82[ASN][1000 genomes]
rs7574437	0.83[ASN][1000 genomes]
rs7582664	0.82[ASN][1000 genomes]
rs7586210	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598116	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602412	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7605180	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308862	0.85[ASN][1000 genomes]
rs956696	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9973416	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279825	ZAP70	cis	Nerve Tibial	GTEx
rs2279825	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98608600-98612800	Active TSS	GM12878-XiMat	blood
2	chr2:98609200-98613400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:98609400-98613000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:98609400-98613200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:98609800-98612000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr2:98609800-98612800	Active TSS	NHLF	lung
7	chr2:98609800-98613200	Active TSS	Aorta	Aorta
8	chr2:98609800-98613400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:98610000-98612800	Active TSS	Fetal Muscle Trunk	muscle
10	chr2:98610000-98613000	Active TSS	Fetal Intestine Small	intestine
11	chr2:98610000-98613000	Active TSS	Fetal Stomach	stomach
12	chr2:98610000-98613200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:98610200-98612800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:98610200-98612800	Active TSS	Fetal Intestine Large	intestine
15	chr2:98610200-98613200	Active TSS	Colonic Mucosa	Colon
16	chr2:98610400-98613000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:98610400-98613200	Active TSS	Stomach Mucosa	stomach
18	chr2:98610400-98613400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr2:98610400-98613400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:98610400-98613400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:98610600-98612800	Active TSS	Pancreas	Pancrea
22	chr2:98610600-98612800	Active TSS	Right Ventricle	heart
23	chr2:98610600-98612800	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr2:98610600-98612800	Active TSS	HMEC	breast
25	chr2:98610600-98612800	Active TSS	HSMM	muscle
26	chr2:98610600-98613000	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr2:98610600-98613000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:98610600-98613200	Active TSS	H1 Cell Line	embryonic stem cell
29	chr2:98610600-98613200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:98610600-98613200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:98610600-98613200	Active TSS	Fetal Kidney	kidney
32	chr2:98610600-98613200	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr2:98610600-98613200	Active TSS	Fetal Lung	lung
34	chr2:98610600-98613200	Active TSS	Left Ventricle	heart
35	chr2:98610600-98613200	Active TSS	Ovary	ovary
36	chr2:98610600-98613200	Active TSS	A549	lung
37	chr2:98610600-98613200	Active TSS	HSMMtube	muscle
38	chr2:98610800-98612800	Active TSS	Primary B cells from peripheral blood	blood
39	chr2:98610800-98612800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:98610800-98612800	Active TSS	Fetal Muscle Leg	muscle
41	chr2:98610800-98612800	Active TSS	Fetal Thymus	thymus
42	chr2:98610800-98612800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:98610800-98612800	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr2:98610800-98612800	Active TSS	NHDF-Ad	bronchial
45	chr2:98610800-98613000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:98610800-98613000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:98610800-98613000	Active TSS	K562	blood
48	chr2:98610800-98613200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:98610800-98613200	Active TSS	Placenta Amnion	Placenta Amnion
50	chr2:98610800-98613200	Active TSS	Psoas Muscle	Psoas

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