Variant report

Variant	rs12669411
Chromosome Location	chr7:100754917-100754918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100749240..100751319-chr7:100753473..100755309,2	K562	blood:
2	chr7:100752460..100757093-chr7:100759104..100763544,6	MCF-7	breast:
3	chr7:100753459..100756167-chr7:100797257..100799197,2	K562	blood:
4	chr7:100749234..100751319-chr7:100752722..100755802,5	K562	blood:
5	chr7:100752598..100755404-chr7:100758782..100760396,2	K562	blood:

Variant related genes	Relation type
ENSG00000106367	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10231438	0.81[CHB][hapmap]
rs10231529	0.81[CHB][hapmap]
rs10953318	0.81[CHB][hapmap]
rs10953321	0.85[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10953322	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11760747	0.82[EUR][1000 genomes]
rs11761555	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11772356	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs11972491	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11973843	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11980635	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12667943	0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs12668231	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs12673732	0.85[EUR][1000 genomes]
rs55996000	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57569772	0.89[EUR][1000 genomes]
rs66492618	0.89[EUR][1000 genomes]
rs67520893	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67568738	0.91[EUR][1000 genomes]
rs67947224	0.85[EUR][1000 genomes]
rs73404898	0.85[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12669411	GATS	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100733600-100755400	Weak transcription	Aorta	Aorta
2	chr7:100747600-100755400	Weak transcription	NHLF	lung
3	chr7:100747600-100760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:100747800-100760600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:100750000-100760200	Weak transcription	Hela-S3	cervix
6	chr7:100750800-100756600	Enhancers	HUVEC	blood vessel
7	chr7:100752400-100755000	Weak transcription	Fetal Stomach	stomach
8	chr7:100752400-100757200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:100752400-100757400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:100752400-100757400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:100752400-100764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:100752600-100755200	Weak transcription	NH-A	brain
13	chr7:100752600-100755400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:100752600-100755400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:100752600-100755600	Weak transcription	Osteobl	bone
16	chr7:100752600-100757400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:100752600-100757400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:100752600-100765400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr7:100752800-100755000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:100752800-100755600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:100752800-100757400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:100752800-100760200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:100752800-100760600	Weak transcription	K562	blood
24	chr7:100753400-100755200	Weak transcription	NHDF-Ad	bronchial
25	chr7:100753400-100757200	Weak transcription	HMEC	breast
26	chr7:100753400-100757200	Weak transcription	NHEK	skin
27	chr7:100753400-100757400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:100753400-100760400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:100753600-100755200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:100753600-100757400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:100754400-100755600	Enhancers	HepG2	liver
32	chr7:100754400-100756400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:100754600-100755000	Enhancers	Psoas Muscle	Psoas
34	chr7:100754600-100755400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:100754600-100755800	Enhancers	HSMMtube	muscle
36	chr7:100754600-100756000	Enhancers	Adipose Nuclei	Adipose
37	chr7:100754600-100756000	Enhancers	Left Ventricle	heart
38	chr7:100754600-100756000	Enhancers	Right Atrium	heart
39	chr7:100754600-100756000	Enhancers	Right Ventricle	heart
40	chr7:100754600-100756200	Enhancers	Ovary	ovary
41	chr7:100754600-100756200	Enhancers	HSMM	muscle
42	chr7:100754600-100756400	Enhancers	Placenta	Placenta
43	chr7:100754600-100757400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr7:100754800-100755400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:100754800-100755400	Weak transcription	A549	lung
46	chr7:100754800-100755600	Enhancers	Lung	lung
47	chr7:100754800-100756000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:100754800-100756000	Enhancers	Spleen	Spleen
49	chr7:100754800-100756200	Enhancers	Fetal Muscle Leg	muscle

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