Variant report

Variant	rs12527139
Chromosome Location	chr6:56398954-56398955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56398077..56400962-chr6:56401619..56403800,2	K562	blood:
2	chr6:56396433..56398982-chr6:56400861..56403143,2	MCF-7	breast:
3	chr6:56390066..56391904-chr6:56396984..56399522,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11753813	0.83[ASN][1000 genomes]
rs11756977	0.81[AMR][1000 genomes]
rs11759493	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11961668	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13194746	0.80[EUR][1000 genomes]
rs13204556	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13219448	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1359068	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1359070	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535610	0.83[ASN][1000 genomes]
rs1535612	0.85[ASN][1000 genomes]
rs16887974	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273973	0.82[ASN][1000 genomes]
rs2273974	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2397226	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34954984	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35671304	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35926142	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4130060	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4143827	0.87[EUR][1000 genomes]
rs4143828	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236139	0.85[EUR][1000 genomes]
rs4236140	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4236141	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4236142	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236143	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236144	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236145	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4283892	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4329120	0.87[EUR][1000 genomes]
rs4331988	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4346846	0.87[EUR][1000 genomes]
rs4454141	0.87[EUR][1000 genomes]
rs4466244	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4472350	0.85[EUR][1000 genomes]
rs4473850	0.88[EUR][1000 genomes]
rs4499917	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4544910	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45486696	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712132	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712133	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4715625	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715626	0.87[EUR][1000 genomes]
rs4715627	0.87[EUR][1000 genomes]
rs4715628	0.87[EUR][1000 genomes]
rs4715629	0.84[EUR][1000 genomes]
rs4715630	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715631	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6459163	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6906792	0.87[EUR][1000 genomes]
rs6907917	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913572	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6914184	0.82[EUR][1000 genomes]
rs6919608	0.85[EUR][1000 genomes]
rs6922770	0.84[EUR][1000 genomes]
rs6939305	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs721475	0.83[ASN][1000 genomes]
rs72877350	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7741295	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743011	0.87[EUR][1000 genomes]
rs7746753	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7755361	0.87[EUR][1000 genomes]
rs7755573	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758054	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759875	0.84[EUR][1000 genomes]
rs7760640	0.84[EUR][1000 genomes]
rs7760695	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761281	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762629	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296848	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296849	0.87[EUR][1000 genomes]
rs9296850	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349825	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9349826	0.87[EUR][1000 genomes]
rs9357921	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357922	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370534	0.81[ASN][1000 genomes]
rs9370535	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9382635	0.83[ASN][1000 genomes]
rs9396214	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9396215	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9396218	0.83[ASN][1000 genomes]
rs9464389	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9475709	0.85[ASN][1000 genomes]
rs9475713	0.87[EUR][1000 genomes]
rs9475714	0.87[EUR][1000 genomes]
rs9475716	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56362800-56400200	Weak transcription	Colonic Mucosa	Colon
3	chr6:56363000-56402200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:56374600-56399600	Weak transcription	Fetal Thymus	thymus
5	chr6:56376400-56407200	Weak transcription	Gastric	stomach
6	chr6:56377200-56404200	Weak transcription	K562	blood
7	chr6:56380600-56401200	Weak transcription	Psoas Muscle	Psoas
8	chr6:56383200-56402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:56384400-56402200	Weak transcription	Small Intestine	intestine
10	chr6:56388000-56402200	Strong transcription	Fetal Intestine Large	intestine
11	chr6:56388200-56401800	Strong transcription	Liver	Liver
12	chr6:56388800-56399600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:56390200-56401400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:56390200-56401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:56390400-56400000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:56390600-56403800	Weak transcription	Thymus	Thymus
17	chr6:56390800-56402400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:56390800-56403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:56391400-56400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:56391400-56400800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:56391400-56400800	Weak transcription	Esophagus	oesophagus
22	chr6:56391400-56400800	Weak transcription	Right Ventricle	heart
23	chr6:56391400-56401200	Weak transcription	Right Atrium	heart
24	chr6:56391400-56402200	Weak transcription	Lung	lung
25	chr6:56391400-56402400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:56391400-56402800	Strong transcription	Fetal Muscle Leg	muscle
27	chr6:56391600-56399800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:56392000-56399200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:56392000-56400800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:56392200-56401600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:56392400-56401600	Strong transcription	Adipose Nuclei	Adipose
32	chr6:56392400-56406200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:56392600-56399400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:56393000-56401400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:56393000-56402000	Weak transcription	Fetal Heart	heart
36	chr6:56393600-56400600	Weak transcription	Fetal Brain Male	brain
37	chr6:56394600-56399600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:56394800-56400800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:56394800-56401000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:56395000-56399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:56395000-56399800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:56395000-56401400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:56395400-56400000	Strong transcription	HSMM	muscle
44	chr6:56395400-56401200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr6:56395400-56401200	Strong transcription	NHDF-Ad	bronchial
46	chr6:56395400-56405200	Weak transcription	Placenta	Placenta
47	chr6:56395600-56401200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:56395800-56399800	Genic enhancers	Rectal Smooth Muscle	rectum
49	chr6:56395800-56401200	Strong transcription	Osteobl	bone
50	chr6:56396000-56401200	Strong transcription	HSMMtube	muscle

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