Variant report

Variant	rs7299866
Chromosome Location	chr12:104576197-104576198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104570742..104573318-chr12:104574956..104577002,2	K562	blood:
2	chr12:104566313..104569865-chr12:104572688..104576807,3	K562	blood:
3	chr12:104530299..104532759-chr12:104575223..104579205,3	MCF-7	breast:
4	chr12:104575420..104578369-chr12:104681215..104683180,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10507174	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes]
rs10507175	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs10735392	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap]
rs10735393	0.86[CEU][hapmap]
rs10745995	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10745996	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10861204	0.86[CEU][hapmap]
rs11111898	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs11111943	0.84[AMR][1000 genomes]
rs12422505	0.85[CHB][hapmap]
rs12423684	0.82[AMR][1000 genomes]
rs12423844	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs12424943	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs12426862	0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs12427339	0.85[CEU][hapmap];0.82[CHD][hapmap]
rs12582966	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs12825521	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17035153	1.00[MKK][hapmap]
rs17035324	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs17192854	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MKK][hapmap]
rs17805748	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17805766	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs2293626	1.00[MKK][hapmap]
rs35142441	0.82[AMR][1000 genomes]
rs4129598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4131750	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap]
rs4131752	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4246264	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4246269	0.86[CEU][hapmap]
rs4246271	0.86[CEU][hapmap]
rs4340124	0.85[CEU][hapmap]
rs4388968	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4406890	0.88[MEX][hapmap]
rs4545635	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[AMR][1000 genomes]
rs4614534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4630362	0.84[CEU][hapmap]
rs4964226	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964227	0.93[CEU][hapmap]
rs4964228	0.93[CEU][hapmap]
rs4964257	0.84[AMR][1000 genomes]
rs4964260	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs4964288	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964728	0.88[MEX][hapmap]
rs4964752	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964761	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964779	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs61939190	0.82[AMR][1000 genomes]
rs61939192	0.82[AMR][1000 genomes]
rs61939221	0.87[ASN][1000 genomes]
rs61939222	0.94[ASN][1000 genomes]
rs6419386	0.84[AMR][1000 genomes]
rs6539128	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539137	0.83[CEU][hapmap]
rs7132418	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138035	0.91[CEU][hapmap]
rs7138317	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs7294997	1.00[CEU][hapmap]
rs7305872	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7314893	0.84[JPT][hapmap]
rs73177991	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7957723	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7957725	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7962423	0.86[CEU][hapmap]
rs7975161	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[MEX][hapmap]
rs7978101	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9739833	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7299866	NFYB	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104571000-104576600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr12:104572600-104576200	Weak transcription	Psoas Muscle	Psoas
3	chr12:104573600-104576800	Enhancers	Colon Smooth Muscle	Colon
4	chr12:104574000-104576800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:104574200-104576600	Enhancers	HMEC	breast
6	chr12:104574200-104576800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:104574200-104576800	Enhancers	NHLF	lung
8	chr12:104574200-104577000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104574200-104577000	Enhancers	Osteobl	bone
10	chr12:104574400-104576400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr12:104574400-104576400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr12:104574400-104576800	Enhancers	Rectal Smooth Muscle	rectum
13	chr12:104574400-104577000	Enhancers	Adipose Nuclei	Adipose
14	chr12:104574600-104576600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:104574600-104576600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:104574800-104576400	Enhancers	Fetal Muscle Leg	muscle
17	chr12:104574800-104576800	Enhancers	Placenta	Placenta
18	chr12:104575000-104576200	Enhancers	NH-A	brain
19	chr12:104575000-104576600	Enhancers	NHDF-Ad	bronchial
20	chr12:104575000-104577400	Enhancers	Pancreas	Pancrea
21	chr12:104575200-104576400	Enhancers	HSMMtube	muscle
22	chr12:104575200-104576800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:104575200-104576800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:104575400-104576800	Enhancers	A549	lung
25	chr12:104575400-104577200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:104575600-104576600	Enhancers	Fetal Muscle Trunk	muscle
27	chr12:104575800-104576200	Enhancers	Fetal Lung	lung
28	chr12:104575800-104576400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr12:104575800-104576400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr12:104575800-104576600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:104576000-104576200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:104576000-104576200	Enhancers	Ovary	ovary
33	chr12:104576000-104576200	Enhancers	Right Atrium	heart
34	chr12:104576000-104576600	Flanking Active TSS	Hela-S3	cervix
35	chr12:104576000-104577400	Enhancers	Aorta	Aorta

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