Variant report

Variant	rs2496386
Chromosome Location	chr6:3868043-3868044
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:3867578..3871255-chr6:3875568..3878363,3	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10447476	0.94[EUR][1000 genomes]
rs11242887	0.87[EUR][1000 genomes]
rs11242889	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755819	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2490034	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490050	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490053	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490054	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490055	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9392531	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1024414	chr6:3862744-3898734	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3855000-3869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:3862200-3868600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:3866000-3869600	Weak transcription	Gastric	stomach
4	chr6:3867200-3868200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:3867200-3868200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:3867200-3868600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:3867200-3869600	Enhancers	Fetal Intestine Large	intestine
8	chr6:3867200-3869600	Enhancers	Fetal Intestine Small	intestine
9	chr6:3867200-3871400	Enhancers	Stomach Mucosa	stomach
10	chr6:3867400-3868800	Enhancers	NHEK	skin
11	chr6:3867400-3869200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:3867600-3868200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:3867600-3868200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:3867600-3868200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:3867600-3868200	Enhancers	NHDF-Ad	bronchial
16	chr6:3867600-3869200	Enhancers	Small Intestine	intestine
17	chr6:3867600-3870200	Enhancers	Fetal Muscle Leg	muscle
18	chr6:3867600-3870600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:3867600-3871200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:3867800-3868200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:3867800-3868800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:3867800-3868800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:3867800-3869200	Enhancers	HMEC	breast
24	chr6:3867800-3869400	Enhancers	Brain Hippocampus Middle	brain
25	chr6:3868000-3868200	Enhancers	Brain Germinal Matrix	brain
26	chr6:3868000-3868200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:3868000-3868600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:3868000-3869000	Flanking Active TSS	Osteobl	bone
29	chr6:3868000-3869600	Enhancers	A549	lung
30	chr6:3868000-3869800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr6:3868000-3871200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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