Variant report

Variant	rs1324129
Chromosome Location	chr6:140385102-140385103
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	chr6:139692663..139698708-chr6:140381231..140386402,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10499217	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10499218	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11751210	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11753982	0.91[EUR][1000 genomes]
rs11754152	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11754864	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11755397	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11758188	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11758612	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11758718	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11759030	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1324127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437498	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1361247	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1408295	0.88[AMR][1000 genomes]
rs1582145	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17069692	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17214668	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17755520	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17755892	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17756503	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17756562	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17756688	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757864	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17811661	0.90[EUR][1000 genomes]
rs17811691	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17811871	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17812354	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812384	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812480	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812617	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812647	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17812736	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933741	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs201279	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs201280	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35441484	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs477737	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895580	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895581	0.85[EUR][1000 genomes]
rs4896502	0.90[EUR][1000 genomes]
rs4896504	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4896505	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4896506	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4896507	0.88[EUR][1000 genomes]
rs496953	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55732492	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55738757	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55834276	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55902158	0.84[EUR][1000 genomes]
rs55907136	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56022257	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56030520	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56202454	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56296431	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58650930	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs593265	0.90[EUR][1000 genomes]
rs59665575	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs597854	0.90[EUR][1000 genomes]
rs608185	0.90[EUR][1000 genomes]
rs615587	0.90[EUR][1000 genomes]
rs638899	0.90[EUR][1000 genomes]
rs645740	0.90[EUR][1000 genomes]
rs656337	0.90[EUR][1000 genomes]
rs656363	0.90[EUR][1000 genomes]
rs657276	0.90[EUR][1000 genomes]
rs659714	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs661507	0.90[EUR][1000 genomes]
rs671038	0.90[EUR][1000 genomes]
rs6925609	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72975808	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72975814	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988718	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988720	0.91[EUR][1000 genomes]
rs72988721	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988724	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988734	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988736	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72988741	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988745	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72988750	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988752	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988753	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988755	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988756	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988758	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988759	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72988761	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72990622	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72990629	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769264	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924090	0.83[EUR][1000 genomes]
rs9484333	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9495619	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9495621	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs953112	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3473486	chr6:140380637-140392373	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	esv3473487	chr6:140380684-140392349	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	esv3473488	chr6:140380690-140392319	Flanking Active TSS Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	esv3473489	chr6:140380774-140392251	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	esv3396540	chr6:140384559-140386457	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140379800-140385200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:140380000-140385200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:140380000-140385800	Enhancers	NHDF-Ad	bronchial
4	chr6:140380600-140386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:140381000-140385200	Enhancers	HSMM	muscle
6	chr6:140381200-140385800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:140382400-140386400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:140383200-140385600	Weak transcription	Ovary	ovary
9	chr6:140384200-140385800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:140384200-140391400	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:140384400-140385800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:140384400-140385800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:140384400-140389600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:140384400-140391800	Weak transcription	Fetal Stomach	stomach
15	chr6:140384400-140391800	Weak transcription	Stomach Mucosa	stomach
16	chr6:140384400-140392800	Weak transcription	Aorta	Aorta
17	chr6:140384600-140385600	Weak transcription	Fetal Intestine Large	intestine
18	chr6:140384600-140385600	Weak transcription	Fetal Intestine Small	intestine
19	chr6:140384600-140391200	Weak transcription	Fetal Lung	lung
20	chr6:140384600-140392000	Weak transcription	HSMMtube	muscle
21	chr6:140384600-140392200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:140384600-140394000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:140384800-140385600	Weak transcription	Adipose Nuclei	Adipose
24	chr6:140385000-140385400	Weak transcription	NHLF	lung
25	chr6:140385000-140389800	Weak transcription	Osteobl	bone

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