Variant report

Variant	rs1468993
Chromosome Location	chr12:46155145-46155146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46122273..46123989-chr12:46154776..46157758,3	MCF-7	breast:
2	chr12:46149877..46152600-chr12:46155145..46158037,2	K562	blood:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1012642	0.96[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs10748432	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880855	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880859	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10880860	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10880871	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11183201	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183243	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12314770	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs12319077	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12320533	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1366024	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1863127	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2059404	0.95[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2193749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2216470	0.81[JPT][hapmap]
rs2408435	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs247918	0.91[CEU][hapmap];0.88[CHB][hapmap]
rs247920	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs247929	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs247930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs35115	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs35117	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs35121	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs35122	0.96[CEU][hapmap];0.80[JPT][hapmap]
rs35125	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]
rs6582574	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67133230	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7132422	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7138997	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724909	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap]
rs7306229	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7315731	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7955891	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7976870	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs997307	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv973961	chr12:46153815-46175394	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46125000-46161200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:46125200-46156000	Weak transcription	Small Intestine	intestine
3	chr12:46126400-46161200	Weak transcription	Aorta	Aorta
4	chr12:46127200-46161200	Weak transcription	HMEC	breast
5	chr12:46127400-46156000	Weak transcription	Adipose Nuclei	Adipose
6	chr12:46128200-46164600	Weak transcription	Esophagus	oesophagus
7	chr12:46129200-46156600	Weak transcription	HepG2	liver
8	chr12:46129400-46156000	Weak transcription	Brain Angular Gyrus	brain
9	chr12:46131200-46160800	Weak transcription	NHEK	skin
10	chr12:46131400-46156200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:46131800-46156000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:46132000-46161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:46132000-46205200	Weak transcription	HSMM	muscle
14	chr12:46132200-46165000	Weak transcription	Lung	lung
15	chr12:46135400-46155400	Weak transcription	HUVEC	blood vessel
16	chr12:46136400-46159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:46136600-46157800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:46136800-46156200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:46137200-46156000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:46137400-46160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:46137400-46163000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:46137400-46174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:46137600-46161800	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:46139000-46156000	Weak transcription	Liver	Liver
25	chr12:46140200-46155200	Weak transcription	Stomach Mucosa	stomach
26	chr12:46140200-46156000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:46140600-46155600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:46141000-46161800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:46142000-46156600	Weak transcription	Hela-S3	cervix
30	chr12:46142000-46168400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:46142200-46156000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:46142200-46161200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:46142400-46156000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:46143000-46156200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:46143200-46156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:46143600-46161400	Weak transcription	Thymus	Thymus
37	chr12:46145200-46156000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:46145400-46156000	Weak transcription	Ovary	ovary
39	chr12:46145400-46167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:46145600-46157200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:46145600-46158200	Weak transcription	Primary T cells from cord blood	blood
42	chr12:46146600-46156000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:46146600-46161200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:46147000-46161200	Weak transcription	Left Ventricle	heart
45	chr12:46147800-46156000	Weak transcription	A549	lung
46	chr12:46148200-46160800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:46148400-46155800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:46148400-46156000	Weak transcription	K562	blood
49	chr12:46148400-46168200	Weak transcription	Psoas Muscle	Psoas
50	chr12:46148600-46155200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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