Variant report

Variant	rs707980
Chromosome Location	chr6:4043847-4043848
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4040955..4045707-chr6:4056854..4061183,4	K562	blood:
2	chr6:4021626..4023220-chr6:4042242..4044660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12174184	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12198921	0.80[GIH][hapmap]
rs1408457	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543355	0.91[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2181894	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2745451	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2745452	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3747761	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747763	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761787	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4266528	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs4466281	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959916	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959918	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4959919	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6900476	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6905475	0.84[ASN][1000 genomes]
rs6906467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910519	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914180	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916982	0.93[ASN][1000 genomes]
rs6921738	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6924389	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6930892	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6933593	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6939049	1.00[JPT][hapmap]
rs6941706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707983	0.94[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707984	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707987	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707988	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs723796	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs73349780	0.86[ASN][1000 genomes]
rs7744603	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763233	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853397	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs853398	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs853399	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853402	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853404	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853409	0.83[ASN][1000 genomes]
rs853410	0.85[ASN][1000 genomes]
rs853411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860477	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860478	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9328215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9328216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392547	0.83[EUR][1000 genomes]
rs9392548	0.83[EUR][1000 genomes]
rs9405217	0.84[CEU][hapmap]
rs9405693	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9405694	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9405695	0.81[LWK][hapmap];0.92[YRI][hapmap]
rs941443	0.93[ASN][1000 genomes]
rs942474	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9503893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs707980	PECI	cis	cerebellum	SCAN
rs707980	PECI	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
5	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:4024600-4059200	Strong transcription	Fetal Thymus	thymus
7	chr6:4027200-4058200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:4030800-4059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:4031000-4059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr6:4033400-4055200	Strong transcription	K562	blood
15	chr6:4033800-4054400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:4035600-4045800	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:4035600-4063600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr6:4035800-4046800	Strong transcription	Fetal Muscle Leg	muscle
21	chr6:4035800-4047200	Strong transcription	Fetal Intestine Large	intestine
22	chr6:4035800-4047200	Strong transcription	Thymus	Thymus
23	chr6:4035800-4051200	Strong transcription	Primary B cells from cord blood	blood
24	chr6:4035800-4052000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr6:4035800-4054400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:4035800-4057400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:4035800-4058400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:4035800-4058600	Strong transcription	Primary T cells from cord blood	blood
29	chr6:4035800-4064600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:4035800-4065000	Strong transcription	Dnd41	blood
31	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:4036000-4045800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:4036000-4058200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:4036400-4047000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:4036400-4055200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:4036600-4055200	Strong transcription	NHEK	skin
41	chr6:4036800-4045200	Strong transcription	Osteobl	bone
42	chr6:4037200-4051000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:4037200-4059400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:4037200-4066200	Strong transcription	Liver	Liver
45	chr6:4037400-4044600	Strong transcription	Fetal Kidney	kidney
46	chr6:4037400-4054200	Strong transcription	NH-A	brain
47	chr6:4037400-4055600	Strong transcription	Hela-S3	cervix
48	chr6:4037400-4058400	Strong transcription	HepG2	liver
49	chr6:4037400-4059400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:4037400-4065800	Strong transcription	Placenta	Placenta

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