Variant report

Variant	rs4964627
Chromosome Location	chr12:104573407-104573408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104530177..104533540-chr12:104569302..104573926,9	MCF-7	breast:
2	chr12:104571599..104574180-chr12:104689003..104690549,2	MCF-7	breast:
3	chr12:104571824..104574318-chr12:104580582..104582719,2	MCF-7	breast:
4	chr12:104566313..104569865-chr12:104572688..104576807,3	K562	blood:
5	chr12:104565973..104567600-chr12:104571102..104573461,2	MCF-7	breast:
6	chr12:104528363..104533397-chr12:104570131..104576145,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10507174	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs10507175	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs10735392	0.86[CEU][hapmap]
rs10735393	0.86[CEU][hapmap]
rs10745995	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs10745996	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs10861204	0.86[CEU][hapmap]
rs11111898	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs11111943	0.84[AMR][1000 genomes]
rs11111955	0.81[CEU][hapmap]
rs12422505	0.85[CHB][hapmap]
rs12423684	0.82[AMR][1000 genomes]
rs12423844	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs12424943	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs12426862	0.81[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs12427339	0.85[CEU][hapmap]
rs12582966	0.86[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs12825521	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs17035324	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17192854	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17805748	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs17805766	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs17806643	0.90[JPT][hapmap]
rs35142441	0.82[AMR][1000 genomes]
rs4129598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131750	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4131752	0.86[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	0.86[CEU][hapmap]
rs4388968	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4475991	0.89[JPT][hapmap]
rs4545635	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4614534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4630362	0.85[CEU][hapmap]
rs4964226	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964227	0.93[CEU][hapmap]
rs4964228	0.93[CEU][hapmap]
rs4964257	0.84[AMR][1000 genomes]
rs4964260	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs4964288	0.86[CEU][hapmap]
rs4964632	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964752	0.86[CEU][hapmap]
rs4964761	0.86[CEU][hapmap]
rs4964779	0.86[CEU][hapmap]
rs61939190	0.82[AMR][1000 genomes]
rs61939192	0.82[AMR][1000 genomes]
rs61939221	0.92[ASN][1000 genomes]
rs61939222	1.00[ASN][1000 genomes]
rs6419386	0.84[AMR][1000 genomes]
rs6539128	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6539137	0.84[CEU][hapmap]
rs7132418	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138035	0.82[CEU][hapmap]
rs7138317	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs7294997	1.00[CEU][hapmap]
rs7299866	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]
rs7305872	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7313063	0.89[JPT][hapmap]
rs7314893	0.84[JPT][hapmap]
rs73177991	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7957723	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7957725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7962423	0.86[CEU][hapmap]
rs7975161	1.00[CHB][hapmap]
rs7978101	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][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

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104571000-104576600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr12:104572200-104574200	Weak transcription	Aorta	Aorta
3	chr12:104572200-104574400	Weak transcription	Adipose Nuclei	Adipose
4	chr12:104572200-104574400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:104572200-104574400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:104572200-104574800	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:104572200-104575200	Weak transcription	Fetal Lung	lung
8	chr12:104572200-104575600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:104572200-104575800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:104572200-104576000	Weak transcription	Right Atrium	heart
11	chr12:104572400-104573600	Enhancers	A549	lung
12	chr12:104572400-104574600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:104572400-104574600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:104572400-104575000	Weak transcription	NH-A	brain
15	chr12:104572400-104575000	Weak transcription	NHDF-Ad	bronchial
16	chr12:104572400-104575200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:104572400-104576000	Weak transcription	Ovary	ovary
18	chr12:104572600-104574000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:104572600-104574200	Weak transcription	HMEC	breast
20	chr12:104572600-104574200	Weak transcription	NHLF	lung
21	chr12:104572600-104574800	Weak transcription	Placenta	Placenta
22	chr12:104572600-104575200	Weak transcription	HSMMtube	muscle
23	chr12:104572600-104576200	Weak transcription	Psoas Muscle	Psoas
24	chr12:104572800-104573800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:104572800-104574200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:104572800-104574200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:104572800-104574200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:104572800-104574200	Weak transcription	Osteobl	bone
29	chr12:104572800-104574400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:104573000-104574000	Weak transcription	Hela-S3	cervix
31	chr12:104573200-104573600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:104573400-104573600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:104573400-104573600	Enhancers	Spleen	Spleen

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