Variant report

Variant	rs7680140
Chromosome Location	chr4:57823457-57823458
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	chr4:57820981..57822823-chr4:57822909..57824563,2	K562	blood:
3	chr4:57819778..57821428-chr4:57822188..57824307,2	MCF-7	breast:
4	chr4:57822867..57826017-chr4:57842371..57845683,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-REST-3	chr4:57823412-57824775	NONHSAT096531

Variant related genes	Relation type
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10866441	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs1105434	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs11133469	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500454	0.85[CEU][hapmap]
rs12641030	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101682	0.94[JPT][hapmap]
rs13108245	0.85[CEU][hapmap]
rs13108570	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130605	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877669	0.82[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap]
rs2170073	1.00[CEU][hapmap]
rs2271808	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3000	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs4339274	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6554398	0.82[CEU][hapmap]
rs6830501	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830774	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838948	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs6847086	0.84[JPT][hapmap]
rs6852110	0.82[CEU][hapmap]
rs7680734	0.82[CEU][hapmap];0.92[MEX][hapmap]
rs7697176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9685436	1.00[CEU][hapmap]

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
rs7680140	POLR2B	cis	parietal	SCAN
rs7680140	TXNDC9	cis	parietal	SCAN

Chromatin state (count:44 , 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	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
29	chr4:57820400-57824200	Weak transcription	Brain Substantia Nigra	brain
30	chr4:57820600-57824000	Weak transcription	Brain Hippocampus Middle	brain
31	chr4:57820600-57824200	Weak transcription	Brain Anterior Caudate	brain
32	chr4:57820600-57824400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:57820600-57827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:57821200-57823800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:57821200-57829400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:57821600-57823600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:57821600-57826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:57822000-57827600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:57822200-57827600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:57822400-57827200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
43	chr4:57823200-57826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:57823400-57824200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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