Variant report

Variant	rs1963666
Chromosome Location	chr4:57820722-57820723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57818770..57822763-chr4:57823881..57826643,6	K562	blood:
2	chr4:57818504..57821226-chr4:57843903..57845654,2	K562	blood:
3	chr4:57819778..57821428-chr4:57822188..57824307,2	MCF-7	breast:
4	chr4:57820686..57823285-chr4:57843864..57846307,2	MCF-7	breast:
5	chr4:57797516..57799149-chr4:57818426..57821000,2	K562	blood:

Variant related genes	Relation type
ENSG00000084092	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10030913	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10866440	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10866441	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1105434	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11729152	0.81[ASN][1000 genomes]
rs11730525	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11734953	0.84[ASN][1000 genomes]
rs11736869	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11736965	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737689	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11933908	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12500454	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12501224	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501990	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12502076	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13108245	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13113802	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119525	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13123018	0.87[EUR][1000 genomes]
rs13131605	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136432	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13146539	0.81[ASN][1000 genomes]
rs13146960	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13149162	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13150593	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13152476	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1877669	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014870	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228991	0.81[ASN][1000 genomes]
rs2412772	0.89[EUR][1000 genomes]
rs3000	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34124552	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34448457	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35267092	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796528	0.81[ASN][1000 genomes]
rs4864606	0.82[ASN][1000 genomes]
rs4864607	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4864608	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55822707	0.82[ASN][1000 genomes]
rs62308135	0.82[ASN][1000 genomes]
rs62308136	0.82[ASN][1000 genomes]
rs62308137	0.81[ASN][1000 genomes]
rs62308155	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554397	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6554398	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6554399	0.81[ASN][1000 genomes]
rs6838948	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6852110	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6854420	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855212	0.81[EUR][1000 genomes]
rs73242609	0.82[ASN][1000 genomes]
rs73242616	0.83[ASN][1000 genomes]
rs7680734	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7685576	0.83[ASN][1000 genomes]
rs7695970	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs781669	0.84[ASN][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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1963666	RP11-738E22.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57798200-57828400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:57798200-57829600	Weak transcription	Pancreas	Pancrea
5	chr4:57798400-57828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:57798600-57828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:57803800-57828400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:57804200-57824200	Weak transcription	NH-A	brain
9	chr4:57804800-57826600	Weak transcription	Liver	Liver
10	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
11	chr4:57805400-57826400	Weak transcription	Primary T cells from cord blood	blood
12	chr4:57805600-57826600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:57805800-57827400	Weak transcription	Placenta	Placenta
14	chr4:57806000-57827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:57806000-57827200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:57806000-57827200	Weak transcription	Thymus	Thymus
17	chr4:57806200-57826600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57808200-57827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:57808600-57827000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:57818800-57826800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:57818800-57827200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr4:57818800-57827400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:57819000-57828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:57819400-57827200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:57819600-57826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:57819800-57821200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:57819800-57821600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
31	chr4:57820400-57824200	Weak transcription	Brain Substantia Nigra	brain
32	chr4:57820600-57824000	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:57820600-57824200	Weak transcription	Brain Anterior Caudate	brain
34	chr4:57820600-57824400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:57820600-57827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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