Variant report

Variant	rs2328863
Chromosome Location	chr6:25194059-25194060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25175400..25178845-chr6:25193942..25196785,3	MCF-7	breast:
2	chr6:25192817..25194714-chr6:25278200..25280696,2	MCF-7	breast:
3	chr6:25193446..25197455-chr6:25200337..25204634,8	MCF-7	breast:
4	chr6:25193165..25196605-chr6:25196765..25200177,4	MCF-7	breast:
5	chr6:25179558..25182381-chr6:25192541..25194103,2	MCF-7	breast:
6	chr6:24719199..24721942-chr6:25193498..25196051,2	MCF-7	breast:
7	chr6:25193162..25195519-chr6:27839293..27841402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198558	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000079691	Chromatin interaction
ENSG00000264238	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000217805	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11965121	1.00[CEU][hapmap]
rs1815095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2328865	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2328866	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2328867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2328869	1.00[CEU][hapmap]
rs2328870	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2328873	1.00[EUR][1000 genomes]
rs4398725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4594940	1.00[CEU][hapmap]
rs4711081	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6456661	1.00[CEU][hapmap]
rs6902634	1.00[CEU][hapmap]
rs7761347	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7773074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9379734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9379737	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25177000-25194600	Weak transcription	Placenta	Placenta
2	chr6:25191800-25194800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr6:25192200-25194200	Enhancers	Rectal Smooth Muscle	rectum
4	chr6:25192400-25195200	Enhancers	HSMMtube	muscle
5	chr6:25192400-25195200	Enhancers	Osteobl	bone
6	chr6:25192600-25194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:25192600-25194800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr6:25192600-25195000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:25192600-25195200	Enhancers	NHLF	lung
10	chr6:25192800-25194400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:25192800-25194800	Enhancers	Fetal Stomach	stomach
12	chr6:25192800-25194800	Enhancers	Right Atrium	heart
13	chr6:25192800-25195000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:25193200-25194400	Flanking Active TSS	HUVEC	blood vessel
15	chr6:25193400-25194600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:25193400-25195400	Enhancers	HSMM	muscle
17	chr6:25193600-25194200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:25193600-25194200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:25193600-25194200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:25193600-25194200	Enhancers	Hela-S3	cervix
21	chr6:25193600-25194400	Enhancers	Stomach Smooth Muscle	stomach
22	chr6:25193600-25194600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:25193600-25194600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:25193600-25194600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:25193600-25194600	Weak transcription	Esophagus	oesophagus
26	chr6:25193600-25194600	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:25193600-25194600	Weak transcription	Left Ventricle	heart
28	chr6:25193600-25194600	Weak transcription	Ovary	ovary
29	chr6:25193600-25194600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:25193600-25194600	Weak transcription	Spleen	Spleen
31	chr6:25193600-25195000	Enhancers	NH-A	brain
32	chr6:25193600-25195400	Enhancers	NHDF-Ad	bronchial
33	chr6:25193600-25196200	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:25193600-25196600	Weak transcription	Aorta	Aorta
35	chr6:25193600-25197200	Weak transcription	Fetal Kidney	kidney
36	chr6:25193600-25202200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:25193800-25194200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:25193800-25194600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:25193800-25195000	Enhancers	Adipose Nuclei	Adipose
40	chr6:25193800-25195000	Enhancers	A549	lung
41	chr6:25193800-25195000	Enhancers	NHEK	skin
42	chr6:25194000-25194400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:25194000-25195000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:25194000-25195000	Enhancers	HMEC	breast

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