Variant report

Variant	rs13125046
Chromosome Location	chr4:57826726-57826727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57775043..57775905-chr4:57826184..57827058,2	MCF-7	breast:
2	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
3	chr4:57826172..57827120-chr4:57904247..57904761,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-REST-4	chr4:57826726-57827705	NONHSAT096532

Variant related genes	Relation type
ENSG00000084093	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10018580	0.82[EUR][1000 genomes]
rs10034163	0.82[EUR][1000 genomes]
rs11947717	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13133792	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1568260	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17087291	0.87[AFR][1000 genomes]
rs17087332	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34278765	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34749389	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35437996	0.81[AFR][1000 genomes]
rs35529818	0.94[EUR][1000 genomes]
rs35706166	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71601666	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7659855	0.87[AMR][1000 genomes]
rs9991234	0.82[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	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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
9	chr4:57805800-57827400	Weak transcription	Placenta	Placenta
10	chr4:57806000-57827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:57806000-57827200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:57806000-57827200	Weak transcription	Thymus	Thymus
13	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:57808200-57827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:57808600-57827000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:57818800-57826800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:57818800-57827200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:57818800-57827400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:57819000-57828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:57819400-57827200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
23	chr4:57820600-57827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:57821200-57829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:57822000-57827600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:57822200-57827600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:57822400-57827200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
30	chr4:57823800-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:57824000-57827800	Weak transcription	Left Ventricle	heart
32	chr4:57824000-57831400	Weak transcription	Right Ventricle	heart
33	chr4:57824400-57827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:57824400-57830400	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:57824600-57827000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:57824600-57827200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:57824600-57828200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr4:57824600-57828400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:57824600-57828400	Weak transcription	Brain Germinal Matrix	brain
40	chr4:57824600-57829000	Weak transcription	Ovary	ovary
41	chr4:57824600-57838400	Weak transcription	Aorta	Aorta
42	chr4:57824800-57827200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:57824800-57827200	Weak transcription	Dnd41	blood
44	chr4:57824800-57828200	Weak transcription	NH-A	brain
45	chr4:57825000-57827800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:57825000-57828200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:57825200-57826800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:57825200-57827200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:57825200-57827200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:57825200-57827200	Weak transcription	HMEC	breast

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