Variant report

Variant	rs7309966
Chromosome Location	chr12:50379667-50379668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50362033..50363685-chr12:50379610..50381169,2	K562	blood:
2	chr12:50378407..50380112-chr12:50416940..50419198,2	K562	blood:
3	chr12:50379485..50381945-chr12:50410290..50412993,2	MCF-7	breast:
4	chr12:50377547..50379840-chr12:50410824..50414125,3	K562	blood:
5	chr12:50377494..50379997-chr12:50383647..50387031,3	K562	blood:

Variant related genes	Relation type
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10161020	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10161120	0.98[EUR][1000 genomes]
rs10875990	0.90[GIH][hapmap]
rs10875992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10875993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169232	0.86[EUR][1000 genomes]
rs11169234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11169256	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169259	0.98[EUR][1000 genomes]
rs11169260	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11835014	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11836389	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12298110	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311010	0.96[EUR][1000 genomes]
rs12317586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292720	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4297542	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55634523	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652312	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55802497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936104	0.98[EUR][1000 genomes]
rs55990533	0.98[EUR][1000 genomes]
rs56099252	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159935	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56232366	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56259551	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57014171	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57045365	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60000653	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60042968	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60456498	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60905953	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs611434	0.94[EUR][1000 genomes]
rs615382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs629754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661823	0.83[EUR][1000 genomes]
rs694851	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs7131715	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306035	0.96[EUR][1000 genomes]
rs7308994	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309480	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7309940	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119648	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73119651	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119660	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119664	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119671	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119681	0.98[EUR][1000 genomes]
rs73119688	0.98[EUR][1000 genomes]
rs73119690	0.98[EUR][1000 genomes]
rs7961683	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7979958	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9325146	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9669608	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription 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	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1827130	chr12:50349765-50379667	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS 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	28 gene(s)	inside rSNPs	diseases
11	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:50367400-50401200	Weak transcription	Gastric	stomach
3	chr12:50369200-50381600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
5	chr12:50372400-50404800	Weak transcription	Spleen	Spleen
6	chr12:50373600-50381600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:50374800-50381600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:50375200-50385400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:50375800-50380800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:50376000-50380200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:50376000-50380200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:50376200-50380000	Enhancers	NHDF-Ad	bronchial
13	chr12:50376200-50383800	Weak transcription	Primary T cells from cord blood	blood
14	chr12:50376400-50385800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:50376600-50380400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr12:50376800-50380000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:50376800-50384000	Weak transcription	Primary B cells from cord blood	blood
18	chr12:50377200-50384600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:50377600-50403200	Weak transcription	Ovary	ovary
20	chr12:50377600-50405600	Strong transcription	Fetal Thymus	thymus
21	chr12:50377800-50384000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:50377800-50399800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:50377800-50400800	Strong transcription	Thymus	Thymus
24	chr12:50378000-50379800	Weak transcription	Dnd41	blood
25	chr12:50378000-50380000	Enhancers	Colon Smooth Muscle	Colon
26	chr12:50378000-50386400	Weak transcription	Adipose Nuclei	Adipose
27	chr12:50378000-50399000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50378200-50379800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:50378200-50379800	Enhancers	Brain Germinal Matrix	brain
30	chr12:50378200-50380000	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:50378200-50381200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr12:50378200-50383600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:50378200-50385800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:50378200-50399200	Weak transcription	Fetal Brain Male	brain
35	chr12:50378200-50400000	Weak transcription	HSMMtube	muscle
36	chr12:50378400-50379800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:50378400-50379800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:50378400-50380000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr12:50378400-50380200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr12:50378400-50380200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:50378400-50382200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:50378400-50385800	Weak transcription	Brain Angular Gyrus	brain
43	chr12:50378400-50385800	Weak transcription	Lung	lung
44	chr12:50378400-50386000	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:50378400-50386600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:50378600-50379800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:50378600-50380000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:50378600-50381000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:50378600-50381400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:50378600-50382000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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