Variant report

Variant	rs1796524
Chromosome Location	chr6:26449219-26449220
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	chr6:26445132..26448422-chr6:26449156..26450907,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111801	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1535278	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs15580	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs1796519	0.80[CEU][hapmap];0.84[YRI][hapmap]
rs2145319	0.93[AMR][1000 genomes]
rs2224379	0.86[AMR][1000 genomes]
rs3736780	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs4713007	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs6905163	0.83[AMR][1000 genomes]
rs6911330	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs6927012	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7745632	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs9366661	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv883499	chr6:26377591-26454454	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3427999	chr6:26378373-26453532	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv462664	chr6:26379537-26451553	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv601184	chr6:26379537-26451553	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv2763996	chr6:26423901-26465384	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1017824	chr6:26425410-26465384	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv1030289	chr6:26428314-26464017	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1033003	chr6:26428314-26465384	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1031229	chr6:26428314-26467182	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv1024483	chr6:26429262-26465384	Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv1034561	chr6:26429262-26467182	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv528172	chr6:26430981-26463660	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
20	nsv1029357	chr6:26432815-26464789	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
21	nsv1023581	chr6:26432815-26465384	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
22	nsv1024222	chr6:26432815-26467182	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
23	nsv1022309	chr6:26434914-26464789	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
24	nsv969359	chr6:26443661-26453241	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1796524	RP11-457M11.5	cis	lung	GTEx
rs1796524	RP11-457M11.5	cis	Thyroid	GTEx
rs1796524	RP11-457M11.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26441200-26449600	Weak transcription	Esophagus	oesophagus
2	chr6:26441200-26457000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:26441200-26457600	Weak transcription	Pancreas	Pancrea
4	chr6:26441400-26453000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:26441400-26455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:26441400-26457000	Weak transcription	Brain Anterior Caudate	brain
7	chr6:26441400-26457400	Weak transcription	Psoas Muscle	Psoas
8	chr6:26441600-26451200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:26441600-26452400	Weak transcription	HSMMtube	muscle
10	chr6:26441600-26452800	Weak transcription	HSMM	muscle
11	chr6:26442200-26455800	Weak transcription	HepG2	liver
12	chr6:26442200-26457400	Weak transcription	Fetal Kidney	kidney
13	chr6:26442400-26457400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:26442400-26457400	Weak transcription	Hela-S3	cervix
15	chr6:26442600-26450000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:26442600-26457400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:26442800-26454600	Weak transcription	NHDF-Ad	bronchial
18	chr6:26443000-26450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:26443000-26457400	Weak transcription	Stomach Mucosa	stomach
20	chr6:26444400-26451000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:26444400-26452000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:26444400-26452600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:26444400-26453000	Strong transcription	Fetal Stomach	stomach
24	chr6:26444600-26452000	Strong transcription	Fetal Muscle Leg	muscle
25	chr6:26444600-26453000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr6:26445000-26449600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:26445000-26454600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:26445200-26449600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:26445200-26457400	Weak transcription	Small Intestine	intestine
30	chr6:26446400-26449600	Weak transcription	Spleen	Spleen
31	chr6:26446400-26449800	Weak transcription	Aorta	Aorta
32	chr6:26446400-26449800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:26446400-26449800	Weak transcription	Thymus	Thymus
34	chr6:26446400-26452600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:26446400-26453000	Weak transcription	Right Atrium	heart
36	chr6:26446400-26454800	Weak transcription	NHLF	lung
37	chr6:26446400-26457200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:26446400-26457400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:26446400-26458200	Weak transcription	Gastric	stomach
40	chr6:26446600-26451400	Strong transcription	Dnd41	blood
41	chr6:26446600-26452000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:26446600-26452800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:26446600-26457000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:26446800-26452400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr6:26447000-26449400	Weak transcription	GM12878-XiMat	blood
46	chr6:26447000-26449800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:26447000-26452600	Strong transcription	Primary T cells from cord blood	blood
48	chr6:26447000-26452800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:26447200-26452000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:26447200-26452000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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