Variant report

Variant	rs781668
Chromosome Location	chr4:57825140-57825141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57822641..57828782-chr4:57838494..57846737,10	K562	blood:
2	chr4:57822867..57826017-chr4:57842371..57845683,4	K562	blood:
3	chr4:57774740..57777531-chr4:57824624..57826659,2	K562	blood:
4	chr4:57818770..57822763-chr4:57823881..57826643,6	K562	blood:

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

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

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];0.88[TSI][hapmap]
rs1277271	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1277284	0.88[CEU][hapmap];0.81[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];0.88[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];0.88[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];0.88[TSI][hapmap]
rs1718839	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]
rs1718886	0.88[CEU][hapmap];0.91[TSI][hapmap];0.81[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	0.82[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];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34659774	0.93[ASN][1000 genomes]
rs35267092	0.81[ASN][1000 genomes]
rs35982175	0.84[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];0.88[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];0.84[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];0.98[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];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs781668	POLR2B	cis	parietal	SCAN
rs781668	IGFBP7	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 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	chr4:57804800-57826600	Weak transcription	Liver	Liver
9	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
10	chr4:57805400-57826400	Weak transcription	Primary T cells from cord blood	blood
11	chr4:57805600-57826600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:57805800-57827400	Weak transcription	Placenta	Placenta
13	chr4:57806000-57827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:57806000-57827200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:57806000-57827200	Weak transcription	Thymus	Thymus
16	chr4:57806200-57826600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:57808200-57827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:57808600-57827000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:57818800-57826800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:57818800-57827200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:57818800-57827400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:57819000-57828400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:57819400-57827200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:57819600-57826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
28	chr4:57820600-57827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:57821200-57829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:57821600-57826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:57822000-57827600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:57822200-57827600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:57822400-57827200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
36	chr4:57823200-57826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:57823600-57825600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:57823800-57825400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:57823800-57825600	Enhancers	Fetal Stomach	stomach
40	chr4:57823800-57826000	Enhancers	Psoas Muscle	Psoas
41	chr4:57823800-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:57824000-57825200	Enhancers	HSMM	muscle
43	chr4:57824000-57825400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:57824000-57825600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:57824000-57826600	Weak transcription	Fetal Thymus	thymus
46	chr4:57824000-57827800	Weak transcription	Left Ventricle	heart
47	chr4:57824000-57831400	Weak transcription	Right Ventricle	heart
48	chr4:57824200-57825200	Enhancers	Brain Angular Gyrus	brain
49	chr4:57824200-57825200	Enhancers	HMEC	breast
50	chr4:57824200-57825400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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