Variant report

Variant	rs1718839
Chromosome Location	chr4:57827206-57827207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
2	chr4:57826815..57829812-chr4:57841300..57844628,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NOA1-1	chr4:57827093-57827539	ENSG00000269949.1
2	lnc-REST-4	chr4:57826726-57827705	NONHSAT096532

Variant related genes	Relation type
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10866440	1.00[JPT][hapmap]
rs10866441	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1105434	1.00[JPT][hapmap]
rs1107675	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11729152	0.88[ASN][1000 genomes]
rs11730321	0.93[JPT][hapmap]
rs11735158	0.83[ASN][1000 genomes]
rs11736192	0.81[ASN][1000 genomes]
rs11736808	0.84[ASN][1000 genomes]
rs11932673	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12500454	1.00[JPT][hapmap]
rs12501224	0.81[ASN][1000 genomes]
rs12502076	0.81[ASN][1000 genomes]
rs12621	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1277271	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1277284	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1277287	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1277288	0.88[ASN][1000 genomes]
rs1277308	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs13108245	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13121176	0.88[ASN][1000 genomes]
rs13136432	0.81[ASN][1000 genomes]
rs1315005	0.88[ASN][1000 genomes]
rs13150593	0.81[ASN][1000 genomes]
rs1403233	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1625691	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17081937	1.00[JPT][hapmap]
rs17087307	0.93[ASN][1000 genomes]
rs17087317	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17087411	0.87[JPT][hapmap]
rs17087414	0.87[JPT][hapmap]
rs1713994	0.83[ASN][1000 genomes]
rs1718831	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs1718886	0.88[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1877669	1.00[JPT][hapmap]
rs1976780	0.93[ASN][1000 genomes]
rs2228991	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2948348	0.84[EUR][1000 genomes]
rs3000	1.00[JPT][hapmap]
rs34124552	0.81[ASN][1000 genomes]
rs34448457	0.81[ASN][1000 genomes]
rs34576794	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34659774	0.93[ASN][1000 genomes]
rs35267092	0.81[ASN][1000 genomes]
rs35982175	0.86[EUR][1000 genomes]
rs3733306	0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3796528	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3806745	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs62308155	0.80[ASN][1000 genomes]
rs6554398	1.00[JPT][hapmap]
rs6554399	0.88[ASN][1000 genomes]
rs6816457	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6838948	1.00[JPT][hapmap]
rs6843644	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs6847086	0.82[JPT][hapmap]
rs6852110	1.00[JPT][hapmap]
rs73242616	0.86[ASN][1000 genomes]
rs7661194	1.00[JPT][hapmap]
rs7668814	0.85[LWK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs7680734	1.00[JPT][hapmap]
rs7685576	0.86[ASN][1000 genomes]
rs781665	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781666	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9942208	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9996331	0.86[AFR][1000 genomes];0.90[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1718839	POLR2B	cis	parietal	SCAN

Chromatin state (count:122 , 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	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:57818800-57827400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:57819000-57828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
15	chr4:57820600-57827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:57821200-57829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:57822000-57827600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:57822200-57827600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
21	chr4:57823800-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:57824000-57827800	Weak transcription	Left Ventricle	heart
23	chr4:57824000-57831400	Weak transcription	Right Ventricle	heart
24	chr4:57824400-57827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:57824400-57830400	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:57824600-57828200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:57824600-57828400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:57824600-57828400	Weak transcription	Brain Germinal Matrix	brain
29	chr4:57824600-57829000	Weak transcription	Ovary	ovary
30	chr4:57824600-57838400	Weak transcription	Aorta	Aorta
31	chr4:57824800-57828200	Weak transcription	NH-A	brain
32	chr4:57825000-57827800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:57825000-57828200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:57825200-57827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:57825200-57827800	Weak transcription	Lung	lung
36	chr4:57825200-57828200	Weak transcription	HSMM	muscle
37	chr4:57825200-57828200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr4:57825200-57829200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:57825200-57829200	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:57825200-57829400	Weak transcription	Brain Angular Gyrus	brain
41	chr4:57825200-57829400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:57825200-57829400	Weak transcription	HSMMtube	muscle
43	chr4:57825200-57829600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:57825200-57829600	Weak transcription	NHEK	skin
45	chr4:57825200-57830600	Weak transcription	Brain Substantia Nigra	brain
46	chr4:57825200-57830800	Weak transcription	HUVEC	blood vessel
47	chr4:57825200-57832400	Weak transcription	A549	lung
48	chr4:57825400-57827400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:57825400-57828000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr4:57825400-57828000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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