Variant report

Variant	rs9378858
Chromosome Location	chr6:4313727-4313728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4312912..4315341-chr6:4776495..4778763,3	MCF-7	breast:
2	chr6:4312864..4313766-chr6:4957300..4958354,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-18	chr6:4313222-4316060	NONHSAT107386

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1034032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752585	1.00[ASN][1000 genomes]
rs11970115	1.00[ASN][1000 genomes]
rs13192123	1.00[ASN][1000 genomes]
rs13197025	1.00[ASN][1000 genomes]
rs13197516	1.00[ASN][1000 genomes]
rs1327990	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327992	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410296	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576142	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002920	1.00[ASN][1000 genomes]
rs2002922	1.00[ASN][1000 genomes]
rs2149097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326409	1.00[YRI][hapmap]
rs34635954	1.00[ASN][1000 genomes]
rs34697725	1.00[ASN][1000 genomes]
rs35281314	1.00[ASN][1000 genomes]
rs35729554	1.00[ASN][1000 genomes]
rs35928057	1.00[ASN][1000 genomes]
rs35940593	1.00[ASN][1000 genomes]
rs36069200	1.00[ASN][1000 genomes]
rs6597033	1.00[ASN][1000 genomes]
rs6597053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912138	1.00[ASN][1000 genomes]
rs6912707	1.00[ASN][1000 genomes]
rs6938649	1.00[ASN][1000 genomes]
rs71555844	1.00[ASN][1000 genomes]
rs7745239	1.00[ASN][1000 genomes]
rs7751774	1.00[ASN][1000 genomes]
rs7769863	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770426	1.00[ASN][1000 genomes]
rs932847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405722	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503947	1.00[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	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	nsv916553	chr6:4269714-4437920	Enhancers Weak transcription 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
30	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
31	nsv600869	chr6:4294450-4430623	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4300200-4316800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:4313200-4314000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:4313200-4314200	Enhancers	NH-A	brain
4	chr6:4313400-4313800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:4313400-4313800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:4313400-4313800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:4313400-4313800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:4313400-4313800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:4313400-4313800	Enhancers	Brain Hippocampus Middle	brain
10	chr6:4313400-4313800	Enhancers	Placenta	Placenta
11	chr6:4313400-4313800	Enhancers	Left Ventricle	heart
12	chr6:4313400-4313800	Enhancers	Pancreas	Pancrea
13	chr6:4313400-4313800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:4313400-4313800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr6:4313400-4313800	Enhancers	Right Ventricle	heart
16	chr6:4313400-4313800	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:4313400-4313800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr6:4313400-4313800	Flanking Active TSS	Hela-S3	cervix
19	chr6:4313400-4313800	Enhancers	HMEC	breast
20	chr6:4313400-4313800	Flanking Active TSS	HSMM	muscle
21	chr6:4313400-4313800	Enhancers	HSMMtube	muscle
22	chr6:4313400-4313800	Flanking Active TSS	HUVEC	blood vessel
23	chr6:4313400-4313800	Flanking Active TSS	NHDF-Ad	bronchial
24	chr6:4313400-4313800	Flanking Active TSS	NHEK	skin
25	chr6:4313400-4313800	Enhancers	NHLF	lung
26	chr6:4313400-4313800	Flanking Active TSS	Osteobl	bone
27	chr6:4313400-4314000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:4313400-4314000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:4313400-4314000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:4313400-4314200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:4313400-4314200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:4313400-4314200	Active TSS	A549	lung
33	chr6:4313600-4313800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:4313600-4313800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:4313600-4313800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:4313600-4313800	Enhancers	Adipose Nuclei	Adipose
37	chr6:4313600-4313800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:4313600-4314000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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