Variant report

Variant	rs4729661
Chromosome Location	chr7:100759964-100759965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100751112..100754051-chr7:100759784..100762309,3	MCF-7	breast:
2	chr7:100752598..100755404-chr7:100758782..100760396,2	K562	blood:
3	chr7:100759553..100761801-chr7:100764388..100767111,2	K562	blood:
4	chr7:100743845..100746782-chr7:100757454..100760117,2	K562	blood:
5	chr7:100752460..100757093-chr7:100759104..100763544,6	MCF-7	breast:
6	chr7:100736428..100739079-chr7:100758952..100761721,2	MCF-7	breast:
7	chr7:100758907..100762284-chr7:100803810..100808280,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260336	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12530725	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12530730	0.88[EUR][1000 genomes]
rs12535610	0.81[AFR][1000 genomes]
rs12536798	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538402	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34144144	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34772825	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35532237	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35664038	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35799997	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36093166	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3890122	0.84[ASN][1000 genomes]
rs4727479	0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729659	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4729662	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4729663	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729664	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs62483748	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465783	0.85[LWK][hapmap]
rs6948536	0.82[MKK][hapmap]
rs6950982	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951404	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955537	0.90[CEU][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6956010	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757722	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7783913	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784462	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784514	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7790022	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
6	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv464649	chr7:100739682-100810983	Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv607972	chr7:100739682-100810983	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4729661	TAF6	cis	cerebellum	SCAN
rs4729661	ZNF789	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100747600-100760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:100747800-100760600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:100750000-100760200	Weak transcription	Hela-S3	cervix
4	chr7:100752400-100764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:100752600-100765400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:100752800-100760200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:100752800-100760600	Weak transcription	K562	blood
8	chr7:100753400-100760400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:100755000-100764800	Weak transcription	Psoas Muscle	Psoas
10	chr7:100755600-100763200	Weak transcription	Lung	lung
11	chr7:100755800-100760200	Weak transcription	HSMMtube	muscle
12	chr7:100755800-100760800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:100756000-100760200	Weak transcription	Left Ventricle	heart
14	chr7:100756000-100760200	Weak transcription	Right Atrium	heart
15	chr7:100756000-100760400	Weak transcription	Right Ventricle	heart
16	chr7:100756000-100763200	Weak transcription	Spleen	Spleen
17	chr7:100756200-100760400	Weak transcription	Ovary	ovary
18	chr7:100757000-100765400	Enhancers	HUVEC	blood vessel
19	chr7:100757600-100770400	Enhancers	Placenta	Placenta
20	chr7:100757800-100760200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:100757800-100760400	Weak transcription	NHLF	lung
22	chr7:100758000-100760200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:100758000-100760200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:100758000-100760400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:100758000-100760600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:100758200-100760200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:100758200-100760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:100758200-100760400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:100758200-100760400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:100758200-100760400	Weak transcription	HMEC	breast
31	chr7:100758200-100760400	Weak transcription	NHEK	skin
32	chr7:100758400-100760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:100759000-100760200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:100759000-100760200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr7:100759000-100760200	Weak transcription	NH-A	brain
36	chr7:100759600-100760200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:100759600-100760400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr7:100759600-100760400	Enhancers	A549	lung
39	chr7:100759600-100765400	Enhancers	NHDF-Ad	bronchial
40	chr7:100759800-100760600	Enhancers	HepG2	liver
41	chr7:100759800-100760800	Enhancers	HSMM	muscle
42	chr7:100759800-100761200	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr7:100759800-100764000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:100759800-100765400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:100759800-100765400	Enhancers	Osteobl	bone

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