Variant report

Variant	rs6664719
Chromosome Location	chr1:94334724-94334725
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94326500..94334861-chr1:94334949..94340833,11	K562	blood:
2	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
3	chr1:94333834..94335597-chr1:94338840..94340897,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10489603	0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782966	0.84[EUR][1000 genomes]
rs10782967	0.84[EUR][1000 genomes]
rs11165020	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165022	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs11165024	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165026	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs12027630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041975	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs12122113	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12134359	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs12137687	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12140446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12143274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12143279	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12563731	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12565614	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565817	0.89[GIH][hapmap]
rs12566531	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739186	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745990	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12752298	0.87[EUR][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs1884018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980083	0.81[CEU][hapmap]
rs2143990	0.86[EUR][1000 genomes]
rs2143992	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2235971	0.86[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];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273166	0.89[CHB][hapmap]
rs2391315	0.82[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747039	0.84[EUR][1000 genomes]
rs2747041	0.84[EUR][1000 genomes]
rs2747043	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747045	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747050	0.84[EUR][1000 genomes]
rs2818160	0.84[EUR][1000 genomes]
rs2818162	0.84[EUR][1000 genomes]
rs2818164	0.86[EUR][1000 genomes]
rs2818169	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3000471	0.86[EUR][1000 genomes]
rs3747965	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];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs4141736	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141737	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240955	0.84[EUR][1000 genomes]
rs4240956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4314890	0.84[EUR][1000 genomes]
rs4350209	0.86[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs4847253	0.80[EUR][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs4847264	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4847265	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681265	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs6685747	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7364910	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8179391	0.84[EUR][1000 genomes]
rs871854	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6664719	RP11-488P3.1	cis	Artery Tibial	GTEx
rs6664719	RP11-488P3.1	cis	Stomach	GTEx
rs6664719	RP11-488P3.1	cis	lung	GTEx
rs6664719	RP11-488P3.1	cis	Thyroid	GTEx
rs6664719	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs6664719	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs6664719	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs6664719	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs6664719	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6664719	RP11-488P3.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94328800-94334800	Weak transcription	Hela-S3	cervix
3	chr1:94329800-94335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
6	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:94330600-94335200	Weak transcription	NHLF	lung
8	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:94330800-94336800	Weak transcription	Spleen	Spleen
10	chr1:94331000-94339000	Weak transcription	Pancreas	Pancrea
11	chr1:94331400-94335200	Weak transcription	Colonic Mucosa	Colon
12	chr1:94331600-94336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:94331600-94336800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:94332400-94342000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:94332600-94336200	Weak transcription	Right Ventricle	heart
16	chr1:94332600-94336800	Weak transcription	Lung	lung
17	chr1:94332800-94337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:94332800-94337000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:94332800-94339600	Weak transcription	Stomach Mucosa	stomach
20	chr1:94332800-94340800	Strong transcription	Left Ventricle	heart
21	chr1:94332800-94341400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:94332800-94341600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:94332800-94341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:94332800-94341800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:94332800-94341800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:94332800-94341800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:94333000-94336800	Weak transcription	Esophagus	oesophagus
30	chr1:94333000-94337000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:94333000-94341600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:94333000-94342000	Strong transcription	Fetal Brain Female	brain
33	chr1:94333200-94334800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:94333200-94334800	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:94333200-94341600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:94333200-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:94333400-94341600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:94333600-94335200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:94333600-94341800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:94333800-94341200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:94333800-94341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:94334000-94340800	Strong transcription	Brain Anterior Caudate	brain
45	chr1:94334000-94341200	Strong transcription	Primary T cells from cord blood	blood
46	chr1:94334000-94341200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:94334000-94341600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:94334000-94341600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:94334000-94341600	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:94334000-94341800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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