Variant report

Variant	rs581829
Chromosome Location	chr7:129094195-129094196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr7:129093983-129094405	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:129093897-129094309	MCF10A-Er-Src	breast:	n/a	chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094134 chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094133 chr7:129094126-129094134
3	MYC	chr7:129094028-129094291	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:129093259-129095004	K562	blood:	n/a	n/a
5	MYC	chr7:129094068-129094266	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr7:129093928-129094304	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr7:129093984-129094286	MCF10A-Er-Src	breast:	n/a	chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094134 chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094133 chr7:129094126-129094134
8	POLR2A	chr7:129094092-129094249	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr7:129093957-129094340	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr7:129093909-129094410	MCF10A-Er-Src	breast:	n/a	chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094134 chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094133 chr7:129094126-129094134
11	FOS	chr7:129093938-129094339	MCF10A-Er-Src	breast:	n/a	chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094134 chr7:129094125-129094135 chr7:129094125-129094135 chr7:129094126-129094133 chr7:129094126-129094134

No.	Distal block	Cell Line	Cell type
1	chr7:129045139..129047193-chr7:129093263..129095853,2	K562	blood:
2	chr7:129078918..129082456-chr7:129089689..129095627,7	K562	blood:
3	chr7:129091760..129094505-chr7:129102793..129105599,2	K562	blood:
4	chr7:129078918..129084090-chr7:129089689..129096186,10	K562	blood:
5	chr7:129089597..129092267-chr7:129093049..129096077,3	K562	blood:
6	chr7:129090117..129092267-chr7:129094044..129096077,2	K562	blood:
7	chr7:129092778..129094548-chr7:129251463..129253115,2	K562	blood:

Variant related genes	Relation type
STRIP2	TF binding region
ENSG00000273329	Chromatin interaction
ENSG00000106459	Chromatin interaction
ENSG00000252280	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10224011	0.82[CHB][hapmap]
rs11768964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[EUR][1000 genomes]
rs11771549	0.85[CHB][hapmap]
rs1272593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402951	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap]
rs2598183	0.85[CHB][hapmap]
rs55832716	0.88[EUR][1000 genomes]
rs587499	0.85[CHB][hapmap]
rs610591	0.82[CHB][hapmap]
rs613068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs613169	0.92[EUR][1000 genomes]
rs632505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs655239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs656981	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs657664	1.00[CHB][hapmap]
rs666499	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676947	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];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs690872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690903	0.80[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs691303	0.84[CHB][hapmap]
rs691325	0.85[CHB][hapmap]
rs691476	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs692132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs692248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692507	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692686	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969620	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs712692	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712693	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7779572	0.81[AFR][1000 genomes]
rs7787531	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap]

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	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv831128	chr7:129063040-129240800	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129075200-129096000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:129075200-129100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:129075200-129108400	Weak transcription	Gastric	stomach
4	chr7:129075400-129102800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:129075400-129105800	Weak transcription	Ovary	ovary
6	chr7:129076000-129095000	Weak transcription	Dnd41	blood
7	chr7:129076000-129110000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:129077400-129109400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:129079200-129095200	Weak transcription	NHLF	lung
10	chr7:129079600-129107200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:129079800-129106400	Weak transcription	NHDF-Ad	bronchial
12	chr7:129080000-129094600	Weak transcription	Hela-S3	cervix
13	chr7:129080000-129104800	Weak transcription	A549	lung
14	chr7:129080000-129128000	Weak transcription	HUVEC	blood vessel
15	chr7:129080600-129101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:129082600-129108400	Weak transcription	Thymus	Thymus
17	chr7:129083800-129112800	Strong transcription	K562	blood
18	chr7:129085800-129103600	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:129086400-129094800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:129087600-129103600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:129088000-129096200	Weak transcription	Psoas Muscle	Psoas
22	chr7:129088400-129098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:129088800-129099800	Weak transcription	HSMMtube	muscle
24	chr7:129089200-129106600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:129089400-129096000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:129089400-129099400	Weak transcription	Spleen	Spleen
27	chr7:129089400-129102600	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:129089400-129108400	Weak transcription	Fetal Lung	lung
29	chr7:129089400-129110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:129089600-129096200	Weak transcription	Fetal Stomach	stomach
31	chr7:129089600-129097800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:129089600-129106400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:129089600-129110200	Weak transcription	Brain Substantia Nigra	brain
34	chr7:129090400-129096000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:129090600-129094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:129091400-129096600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:129091400-129097000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:129091400-129104000	Strong transcription	Brain Anterior Caudate	brain
39	chr7:129091600-129109200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr7:129091800-129094400	Enhancers	Pancreas	Pancrea
41	chr7:129091800-129095000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:129091800-129095200	Weak transcription	Fetal Brain Female	brain
43	chr7:129091800-129108800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:129092000-129094800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:129092200-129094200	Weak transcription	HepG2	liver
46	chr7:129092200-129094800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:129092200-129096000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr7:129092400-129094600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr7:129092400-129094800	Enhancers	HMEC	breast
50	chr7:129092600-129109200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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