Variant report

Variant	rs11741143
Chromosome Location	chr5:79278596-79278597
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	chr5:79265623..79267181-chr5:79277439..79279231,2	MCF-7	breast:
2	chr5:79269309..79272565-chr5:79276555..79279232,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10035728	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041404	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10043116	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060444	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062607	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs10065778	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10066471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10071601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077238	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1017996	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1017997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1017998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1032341	0.80[EUR][1000 genomes]
rs1032342	0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs11748289	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13354864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1370987	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438739	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2404708	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451929	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2451930	0.83[EUR][1000 genomes]
rs2471104	0.95[JPT][hapmap]
rs2471105	0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2471107	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2471108	0.83[EUR][1000 genomes]
rs2471109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs405878	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs422690	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6453494	0.92[EUR][1000 genomes]
rs6453495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860568	0.84[EUR][1000 genomes]
rs6865678	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6868916	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6870377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873684	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882768	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6887873	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6892826	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7446065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7707036	0.89[ASN][1000 genomes]
rs7734858	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923634	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs923636	0.82[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs9293795	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs963423	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs963424	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv2763465	chr5:79274595-79278596	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11741143	ACOT12	cis	cerebellum	SCAN
rs11741143	THBS4	cis	cerebellum	SCAN
rs11741143	MTX3	Cis_1M	lymphoblastoid	RTeQTL
rs11741143	THBS4	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79260600-79286200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:79269000-79286400	Weak transcription	Thymus	Thymus
3	chr5:79269400-79279200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr5:79269800-79279200	Weak transcription	Brain Substantia Nigra	brain
5	chr5:79269800-79279400	Weak transcription	Lung	lung
6	chr5:79269800-79281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:79269800-79286000	Weak transcription	Fetal Heart	heart
8	chr5:79270000-79286000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:79270200-79286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:79270800-79284800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:79271000-79286400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:79271200-79279400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:79271200-79280400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:79271200-79281000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:79271200-79282000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:79271200-79285200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:79271200-79285800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:79271200-79285800	Weak transcription	NHLF	lung
19	chr5:79271400-79284000	Weak transcription	HSMMtube	muscle
20	chr5:79271400-79285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:79271400-79286000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:79271400-79286000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:79271600-79280800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:79271600-79286000	Weak transcription	HUVEC	blood vessel
25	chr5:79272200-79279400	Weak transcription	Spleen	Spleen
26	chr5:79272200-79286400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:79272400-79279400	Weak transcription	Right Ventricle	heart
28	chr5:79272400-79285000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:79272400-79286400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:79272400-79286400	Weak transcription	Pancreas	Pancrea
31	chr5:79272600-79284800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:79272600-79285000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr5:79272600-79285000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:79272600-79285200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:79272600-79286000	Weak transcription	Small Intestine	intestine
36	chr5:79272600-79286400	Weak transcription	Gastric	stomach
37	chr5:79272800-79279400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:79272800-79285000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:79272800-79285400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:79273000-79284600	Strong transcription	Fetal Intestine Large	intestine
41	chr5:79273000-79284800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:79273000-79284800	Strong transcription	Adipose Nuclei	Adipose
43	chr5:79273400-79286000	Weak transcription	Aorta	Aorta
44	chr5:79273600-79284600	Strong transcription	Placenta	Placenta
45	chr5:79274000-79286400	Weak transcription	Esophagus	oesophagus
46	chr5:79274200-79278600	Weak transcription	Brain Germinal Matrix	brain
47	chr5:79274200-79278800	Weak transcription	Fetal Brain Female	brain
48	chr5:79274200-79279200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:79274200-79279400	Weak transcription	A549	lung
50	chr5:79274200-79281200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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