Variant report

Variant	rs9405742
Chromosome Location	chr6:4444230-4444231
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	chr6:4443894..4445765-chr6:4448052..4449778,2	MCF-7	breast:

Extended variants
information (count: 193 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs1010638	0.89[ASN][1000 genomes]
rs10447477	0.89[ASN][1000 genomes]
rs10447478	0.88[ASN][1000 genomes]
rs10458172	0.93[ASN][1000 genomes]
rs10458173	0.93[ASN][1000 genomes]
rs10458174	0.93[ASN][1000 genomes]
rs10900958	0.93[ASN][1000 genomes]
rs10900959	0.93[ASN][1000 genomes]
rs10900960	0.93[ASN][1000 genomes]
rs10900961	0.93[ASN][1000 genomes]
rs10900962	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11242933	0.93[ASN][1000 genomes]
rs11242934	0.93[ASN][1000 genomes]
rs11242935	0.93[ASN][1000 genomes]
rs11242936	0.93[ASN][1000 genomes]
rs11242937	0.93[ASN][1000 genomes]
rs11242938	0.95[ASN][1000 genomes]
rs11242939	0.93[ASN][1000 genomes]
rs11242942	0.83[ASN][1000 genomes]
rs11242943	0.85[ASN][1000 genomes]
rs11242944	0.95[ASN][1000 genomes]
rs11242946	0.96[ASN][1000 genomes]
rs11242947	0.96[ASN][1000 genomes]
rs11242948	0.91[ASN][1000 genomes]
rs11242950	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11755069	0.93[ASN][1000 genomes]
rs11755676	0.81[AFR][1000 genomes]
rs12191559	0.94[ASN][1000 genomes]
rs12200144	0.93[ASN][1000 genomes]
rs12203267	0.91[ASN][1000 genomes]
rs12207441	0.91[ASN][1000 genomes]
rs12207864	0.91[ASN][1000 genomes]
rs12210818	0.93[ASN][1000 genomes]
rs12211520	0.96[ASN][1000 genomes]
rs12211781	0.91[ASN][1000 genomes]
rs12529480	0.96[ASN][1000 genomes]
rs1265298	0.94[ASN][1000 genomes]
rs1265299	0.89[ASN][1000 genomes]
rs1265303	0.95[ASN][1000 genomes]
rs1265304	0.89[ASN][1000 genomes]
rs1265305	0.89[ASN][1000 genomes]
rs12660869	0.96[ASN][1000 genomes]
rs12663036	0.91[ASN][1000 genomes]
rs12664576	0.88[ASN][1000 genomes]
rs12665814	0.91[ASN][1000 genomes]
rs13213475	0.93[ASN][1000 genomes]
rs13214482	0.88[ASN][1000 genomes]
rs1330783	0.92[ASN][1000 genomes]
rs1330784	0.93[ASN][1000 genomes]
rs1330786	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1330787	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1330788	0.96[ASN][1000 genomes]
rs1330789	0.96[ASN][1000 genomes]
rs1330791	0.95[ASN][1000 genomes]
rs1411654	0.95[ASN][1000 genomes]
rs1411656	0.93[ASN][1000 genomes]
rs1581971	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1581972	0.93[ASN][1000 genomes]
rs1590939	0.93[ASN][1000 genomes]
rs17510496	0.91[ASN][1000 genomes]
rs17510539	0.91[ASN][1000 genomes]
rs17570029	0.91[ASN][1000 genomes]
rs2026183	0.88[ASN][1000 genomes]
rs2026184	0.88[ASN][1000 genomes]
rs2026185	0.88[ASN][1000 genomes]
rs2150233	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2150234	0.91[ASN][1000 genomes]
rs2183497	0.93[ASN][1000 genomes]
rs2225369	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2326490	0.88[ASN][1000 genomes]
rs2875944	0.91[ASN][1000 genomes]
rs4286821	0.95[ASN][1000 genomes]
rs4403297	0.91[ASN][1000 genomes]
rs4481463	0.91[ASN][1000 genomes]
rs4513847	0.93[ASN][1000 genomes]
rs4534025	0.91[ASN][1000 genomes]
rs4621669	0.93[ASN][1000 genomes]
rs4959287	0.93[ASN][1000 genomes]
rs4959288	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4959293	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4959294	0.90[ASN][1000 genomes]
rs4959960	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4959961	0.95[ASN][1000 genomes]
rs4959962	0.94[ASN][1000 genomes]
rs4959965	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4959966	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4959968	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4959969	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4959970	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4959973	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4959974	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4959976	0.98[ASN][1000 genomes]
rs4959978	0.90[ASN][1000 genomes]
rs5002972	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59075559	0.93[ASN][1000 genomes]
rs59425532	0.95[ASN][1000 genomes]
rs60109220	0.91[ASN][1000 genomes]
rs6597055	0.93[ASN][1000 genomes]
rs6597060	0.89[ASN][1000 genomes]
rs6597066	0.96[ASN][1000 genomes]
rs6597067	0.96[ASN][1000 genomes]
rs6597068	0.96[ASN][1000 genomes]
rs6597069	0.95[ASN][1000 genomes]
rs66815625	0.96[ASN][1000 genomes]
rs67284074	0.96[ASN][1000 genomes]
rs67655715	0.91[ASN][1000 genomes]
rs6902044	0.93[ASN][1000 genomes]
rs6904462	0.96[ASN][1000 genomes]
rs6908618	0.85[ASN][1000 genomes]
rs6908628	0.89[ASN][1000 genomes]
rs6911222	0.91[ASN][1000 genomes]
rs6912116	0.91[ASN][1000 genomes]
rs6912489	0.91[ASN][1000 genomes]
rs6912741	0.93[ASN][1000 genomes]
rs6913210	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6914316	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6917196	0.91[ASN][1000 genomes]
rs6920549	0.93[ASN][1000 genomes]
rs6923978	0.96[ASN][1000 genomes]
rs6924842	0.96[ASN][1000 genomes]
rs6926926	0.91[ASN][1000 genomes]
rs6927710	0.93[ASN][1000 genomes]
rs6929358	0.93[ASN][1000 genomes]
rs6930889	0.88[ASN][1000 genomes]
rs6931444	0.91[ASN][1000 genomes]
rs6934676	0.91[ASN][1000 genomes]
rs6937848	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7450619	0.93[ASN][1000 genomes]
rs7453615	0.95[ASN][1000 genomes]
rs7454057	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7750156	0.93[ASN][1000 genomes]
rs7752768	0.95[ASN][1000 genomes]
rs7754765	0.90[ASN][1000 genomes]
rs7756945	0.91[ASN][1000 genomes]
rs7760765	0.88[ASN][1000 genomes]
rs7765880	0.91[ASN][1000 genomes]
rs7766314	0.91[ASN][1000 genomes]
rs911568	0.95[ASN][1000 genomes]
rs911569	0.95[ASN][1000 genomes]
rs9328251	0.88[ASN][1000 genomes]
rs9328252	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378400	0.91[ASN][1000 genomes]
rs9378872	0.91[ASN][1000 genomes]
rs9378873	0.92[ASN][1000 genomes]
rs9378874	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9378875	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9378876	0.93[ASN][1000 genomes]
rs9378877	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392046	0.96[ASN][1000 genomes]
rs9392047	0.96[ASN][1000 genomes]
rs9392594	0.91[ASN][1000 genomes]
rs9392596	0.93[ASN][1000 genomes]
rs9392597	0.91[ASN][1000 genomes]
rs9405731	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9405738	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9504074	0.93[ASN][1000 genomes]
rs9504076	0.89[ASN][1000 genomes]
rs9504090	0.86[ASN][1000 genomes]
rs9504091	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9504093	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9504094	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9504096	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1030655	chr6:4257190-4473701	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv538108	chr6:4257190-4473701	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1030840	chr6:4257390-4473562	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv538109	chr6:4257390-4473562	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv1026890	chr6:4259075-4471635	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv1030588	chr6:4264933-4455210	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv1021257	chr6:4264933-4473384	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv538110	chr6:4264933-4473384	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv1016621	chr6:4277411-4473384	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
29	nsv883413	chr6:4371622-4474114	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
30	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4442600-4447400	Weak transcription	NHLF	lung
2	chr6:4442600-4449600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:4442800-4446200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:4442800-4446400	Weak transcription	Placenta	Placenta
5	chr6:4442800-4447400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:4442800-4447400	Weak transcription	HSMMtube	muscle
7	chr6:4442800-4459000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:4443000-4446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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