Variant report

Variant	rs2281428
Chromosome Location	chr20:23400050-23400051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23336395..23338655-chr20:23399846..23402203,2	K562	blood:
2	chr20:23398847..23400771-chr20:23575954..23577563,2	K562	blood:
3	chr20:23331362..23333588-chr20:23399396..23402095,2	K562	blood:
4	chr20:23330877..23333588-chr20:23399396..23402604,5	K562	blood:
5	chr20:23328647..23330996-chr20:23399236..23401652,2	K562	blood:
6	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:
7	chr20:23388261..23390849-chr20:23399031..23401935,2	K562	blood:
8	chr20:23329969..23332172-chr20:23397357..23400291,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232645	Chromatin interaction
ENSG00000234832	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000132661	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12625160	0.85[JPT][hapmap]
rs12625164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.85[JPT][hapmap]
rs17757228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17757442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17830281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2277765	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2295238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34648279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3746733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3761274	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3827086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55851398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56094936	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56334525	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036423	0.80[JPT][hapmap]
rs6036424	0.84[JPT][hapmap]
rs6048803	0.89[JPT][hapmap]
rs6106669	0.84[JPT][hapmap]
rs6114094	0.89[JPT][hapmap]
rs6114142	0.84[JPT][hapmap]
rs6114144	0.84[JPT][hapmap]
rs6132599	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132610	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6132621	0.85[JPT][hapmap]
rs6132622	0.84[JPT][hapmap]
rs6132623	0.84[JPT][hapmap]
rs6132631	0.80[JPT][hapmap]
rs6137901	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137948	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137957	0.85[JPT][hapmap]
rs6137959	0.85[JPT][hapmap]
rs6137961	0.85[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8183135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2281428	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23372800-23400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23375800-23400200	Weak transcription	Fetal Brain Male	brain
3	chr20:23376600-23400400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr20:23379000-23400200	Weak transcription	Primary B cells from cord blood	blood
5	chr20:23379000-23400400	Weak transcription	Brain Substantia Nigra	brain
6	chr20:23379200-23400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr20:23382000-23400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:23382200-23400200	Weak transcription	A549	lung
9	chr20:23383000-23400400	Weak transcription	Thymus	Thymus
10	chr20:23383600-23400400	Weak transcription	Fetal Thymus	thymus
11	chr20:23385200-23400400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:23385400-23400400	Weak transcription	Aorta	Aorta
13	chr20:23387000-23400400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr20:23389200-23400400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr20:23389600-23400200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr20:23390800-23400400	Weak transcription	Lung	lung
17	chr20:23391200-23400400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr20:23391200-23400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr20:23391200-23400800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr20:23391400-23400400	Weak transcription	Placenta	Placenta
21	chr20:23392400-23400400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:23392800-23400400	Weak transcription	Right Ventricle	heart
23	chr20:23393000-23400400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:23393800-23400400	Weak transcription	Right Atrium	heart
25	chr20:23395000-23401000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr20:23396400-23400600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr20:23396600-23400600	Weak transcription	Esophagus	oesophagus
28	chr20:23396800-23400400	Weak transcription	Ovary	ovary
29	chr20:23397000-23400400	Weak transcription	Left Ventricle	heart
30	chr20:23397000-23400400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr20:23397000-23400800	Weak transcription	Pancreas	Pancrea
32	chr20:23397000-23401000	Weak transcription	Gastric	stomach
33	chr20:23397400-23400400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr20:23398200-23400200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr20:23398200-23400400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr20:23398200-23400600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr20:23398600-23400200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr20:23398600-23400400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:23398600-23400400	Enhancers	Colon Smooth Muscle	Colon
40	chr20:23398600-23400400	Enhancers	Fetal Heart	heart
41	chr20:23398800-23400200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr20:23398800-23400200	Weak transcription	Fetal Kidney	kidney
43	chr20:23398800-23400600	Weak transcription	Fetal Stomach	stomach
44	chr20:23399000-23400200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr20:23399200-23400400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr20:23399600-23400200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:23399600-23400200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr20:23399600-23400200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr20:23399600-23400400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr20:23399600-23400400	Enhancers	Liver	Liver

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