Variant report

Variant	rs13146960
Chromosome Location	chr4:57790108-57790109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57739739..57741859-chr4:57787716..57790599,2	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]
rs10008356	0.89[ASN][1000 genomes]
rs10030913	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866440	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10866441	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1105434	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11730321	0.87[ASN][1000 genomes]
rs11730476	0.87[ASN][1000 genomes]
rs11730525	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734953	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11736192	0.88[ASN][1000 genomes]
rs11736869	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11736965	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737689	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11933908	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11941568	0.85[EUR][1000 genomes]
rs12500454	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501224	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12501990	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502076	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13108245	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113802	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13116564	0.94[ASN][1000 genomes]
rs13119525	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13131605	0.85[ASN][1000 genomes]
rs13136432	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149162	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13150593	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152476	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13353552	0.93[ASN][1000 genomes]
rs1877669	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1963666	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002153	0.90[ASN][1000 genomes]
rs2014870	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2090962	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228991	0.81[ASN][1000 genomes]
rs3000	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34124552	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34448457	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35267092	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3796528	0.81[ASN][1000 genomes]
rs3806745	0.87[ASN][1000 genomes]
rs4276341	0.94[ASN][1000 genomes]
rs4864606	0.96[ASN][1000 genomes]
rs4864607	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864608	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865156	0.87[ASN][1000 genomes]
rs4865157	0.89[ASN][1000 genomes]
rs4865158	0.88[ASN][1000 genomes]
rs4865159	0.90[ASN][1000 genomes]
rs4865160	0.90[ASN][1000 genomes]
rs55822707	0.95[ASN][1000 genomes]
rs56122758	0.87[ASN][1000 genomes]
rs62308110	0.87[ASN][1000 genomes]
rs62308111	0.87[ASN][1000 genomes]
rs62308135	0.96[ASN][1000 genomes]
rs62308136	0.96[ASN][1000 genomes]
rs62308137	0.95[ASN][1000 genomes]
rs62308155	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554393	0.89[ASN][1000 genomes]
rs6554394	0.89[ASN][1000 genomes]
rs6554397	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554399	0.81[ASN][1000 genomes]
rs6816950	0.87[ASN][1000 genomes]
rs6835102	0.85[ASN][1000 genomes]
rs6835108	0.85[ASN][1000 genomes]
rs6838948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839845	0.85[ASN][1000 genomes]
rs6840805	0.87[ASN][1000 genomes]
rs6852110	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6854420	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6855212	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857005	0.85[ASN][1000 genomes]
rs6857226	0.85[ASN][1000 genomes]
rs6858216	0.87[ASN][1000 genomes]
rs71601656	0.81[ASN][1000 genomes]
rs729844	0.94[ASN][1000 genomes]
rs73242609	0.96[ASN][1000 genomes]
rs7666804	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667302	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7667744	0.85[EUR][1000 genomes]
rs7680734	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695970	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs899630	0.85[EUR][1000 genomes]
rs899631	0.85[EUR][1000 genomes]
rs899632	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9684742	0.94[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1797793	chr4:57786450-57793425	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57777000-57795800	Weak transcription	A549	lung
2	chr4:57777000-57796600	Weak transcription	Fetal Brain Female	brain
3	chr4:57777000-57797000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:57777200-57793400	Weak transcription	HMEC	breast
5	chr4:57777200-57796600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57777200-57796600	Weak transcription	Aorta	Aorta
7	chr4:57777200-57796800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:57777200-57797200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:57777600-57796000	Weak transcription	Brain Anterior Caudate	brain
10	chr4:57777600-57796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:57777600-57796600	Weak transcription	Colonic Mucosa	Colon
12	chr4:57777600-57803200	Weak transcription	NHDF-Ad	bronchial
13	chr4:57777600-57805600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:57777600-57806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:57778000-57791800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:57778000-57796000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:57778000-57796000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:57778000-57796600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:57778000-57797000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:57778200-57796200	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:57778200-57796800	Weak transcription	NHLF	lung
22	chr4:57778400-57795400	Weak transcription	HSMMtube	muscle
23	chr4:57778400-57796000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:57778400-57800200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:57778400-57800200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:57778400-57801000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:57778800-57795800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:57779000-57804600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:57779200-57799200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:57779800-57796000	Weak transcription	Small Intestine	intestine
31	chr4:57779800-57797600	Weak transcription	Fetal Brain Male	brain
32	chr4:57779800-57799600	Weak transcription	Right Atrium	heart
33	chr4:57780200-57793000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:57780400-57800400	Strong transcription	Fetal Thymus	thymus
35	chr4:57780800-57795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:57780800-57808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:57781000-57791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:57781000-57796800	Weak transcription	Spleen	Spleen
39	chr4:57781000-57799600	Weak transcription	Psoas Muscle	Psoas
40	chr4:57781800-57801400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:57782200-57790800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:57782400-57792400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:57782400-57796000	Weak transcription	Hela-S3	cervix
44	chr4:57782800-57792600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:57782800-57796800	Weak transcription	Pancreas	Pancrea
46	chr4:57783000-57792200	Strong transcription	Placenta	Placenta
47	chr4:57783000-57792800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:57783000-57798400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:57783200-57792200	Strong transcription	Liver	Liver
50	chr4:57783200-57796200	Weak transcription	Fetal Heart	heart

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