Variant report

Variant	rs4144129
Chromosome Location	chr6:25193064-25193065
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	chr6:25192817..25194714-chr6:25278200..25280696,2	MCF-7	breast:
2	chr6:25179558..25182381-chr6:25192541..25194103,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction
ENSG00000217805	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13198274	0.83[CEU][hapmap]
rs13198939	0.83[CEU][hapmap]
rs13202933	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1815096	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35624158	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36084063	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58333539	0.92[ASN][1000 genomes]
rs6456657	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456658	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68094488	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6938383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295648	0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs9295650	0.85[JPT][hapmap]
rs9393622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393624	0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4144129	HIST1H2BI	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25177000-25194600	Weak transcription	Placenta	Placenta
2	chr6:25191800-25193200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25191800-25194800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr6:25192200-25193600	Enhancers	Colon Smooth Muscle	Colon
5	chr6:25192200-25194200	Enhancers	Rectal Smooth Muscle	rectum
6	chr6:25192400-25193200	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr6:25192400-25193200	Enhancers	HUVEC	blood vessel
8	chr6:25192400-25195200	Enhancers	HSMMtube	muscle
9	chr6:25192400-25195200	Enhancers	Osteobl	bone
10	chr6:25192600-25193200	Enhancers	NHEK	skin
11	chr6:25192600-25193400	Enhancers	A549	lung
12	chr6:25192600-25193600	Flanking Active TSS	Hela-S3	cervix
13	chr6:25192600-25193600	Enhancers	HMEC	breast
14	chr6:25192600-25194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr6:25192600-25194800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr6:25192600-25195000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:25192600-25195200	Enhancers	NHLF	lung
18	chr6:25192800-25193200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:25192800-25193200	Enhancers	NH-A	brain
20	chr6:25192800-25193400	Enhancers	Adipose Nuclei	Adipose
21	chr6:25192800-25193400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:25192800-25193400	Flanking Active TSS	HSMM	muscle
23	chr6:25192800-25193600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:25192800-25193600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:25192800-25193600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:25192800-25193600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:25192800-25193600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:25192800-25193600	Enhancers	Aorta	Aorta
29	chr6:25192800-25193600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:25192800-25193600	Enhancers	Colonic Mucosa	Colon
31	chr6:25192800-25193600	Enhancers	Esophagus	oesophagus
32	chr6:25192800-25193600	Enhancers	Fetal Kidney	kidney
33	chr6:25192800-25193600	Enhancers	Fetal Lung	lung
34	chr6:25192800-25193600	Enhancers	Fetal Muscle Leg	muscle
35	chr6:25192800-25193600	Enhancers	Left Ventricle	heart
36	chr6:25192800-25193600	Enhancers	Ovary	ovary
37	chr6:25192800-25193600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:25192800-25193600	Enhancers	Small Intestine	intestine
39	chr6:25192800-25193600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr6:25192800-25193800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:25192800-25194000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:25192800-25194400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:25192800-25194800	Enhancers	Fetal Stomach	stomach
44	chr6:25192800-25194800	Enhancers	Right Atrium	heart
45	chr6:25192800-25195000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:25193000-25193200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:25193000-25193400	Active TSS	Stomach Smooth Muscle	stomach
48	chr6:25193000-25193400	Enhancers	Thymus	Thymus
49	chr6:25193000-25193600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:25193000-25193600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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