Variant report

Variant	rs12525919
Chromosome Location	chr6:3988758-3988759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:3985992..3988806-chr6:4017298..4019133,2	MCF-7	breast:
2	chr6:3981805..3984986-chr6:3987374..3990982,3	K562	blood:
3	chr6:3987504..3989265-chr6:4020369..4023085,2	MCF-7	breast:
4	chr6:3988050..3991356-chr6:3993338..3995417,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-7	chr6:3987967-3989239	NONHSAT107259

Variant related genes	Relation type
ENSG00000230648	Chromatin interaction
ENSG00000145965	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12524454	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525663	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324450	0.83[MEX][hapmap]
rs17137399	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959268	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959269	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644150	0.82[MEX][hapmap]
rs6929755	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751076	0.87[AFR][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	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
3	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
4	esv1800199	chr6:3986611-4014872	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12525919	C1orf25	trans	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3976400-3990800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:3978600-3991000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr6:3978600-3991000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:3978800-3991000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:3978800-3991000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:3978800-3991000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:3979000-3990600	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:3979000-3990800	Weak transcription	HSMM	muscle
9	chr6:3979000-3991000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:3979000-4003200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:3979200-3990600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:3979200-3991000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:3979400-3990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:3980600-4003600	Weak transcription	Primary B cells from cord blood	blood
15	chr6:3980800-3990800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:3982400-3990600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:3983000-3991000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:3983800-3990800	Weak transcription	Ovary	ovary
19	chr6:3985400-4011000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:3985800-3990800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:3986800-3990800	Weak transcription	Esophagus	oesophagus
22	chr6:3987000-3990600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:3987000-3991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:3987000-3991000	Weak transcription	Fetal Thymus	thymus
25	chr6:3987200-3990600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:3987400-3990600	Weak transcription	Right Atrium	heart
27	chr6:3987400-3990800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:3987600-3990200	Weak transcription	Placenta	Placenta
29	chr6:3987600-3990400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:3987600-3990400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:3987600-3990600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:3987600-3990800	Weak transcription	Aorta	Aorta
33	chr6:3987600-3990800	Weak transcription	Psoas Muscle	Psoas
34	chr6:3987600-3991000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:3987600-3991000	Weak transcription	Fetal Intestine Large	intestine
36	chr6:3987600-3991000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:3987600-3991000	Weak transcription	Stomach Mucosa	stomach
38	chr6:3987800-3990600	Weak transcription	Adipose Nuclei	Adipose
39	chr6:3987800-3990600	Weak transcription	Osteobl	bone
40	chr6:3987800-3990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:3987800-3990800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:3987800-3990800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:3987800-3990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:3987800-3990800	Weak transcription	Fetal Intestine Small	intestine
45	chr6:3987800-3990800	Weak transcription	Fetal Lung	lung
46	chr6:3987800-3990800	Weak transcription	Left Ventricle	heart
47	chr6:3987800-3990800	Weak transcription	Pancreas	Pancrea
48	chr6:3987800-3990800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:3987800-3990800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:3987800-3990800	Weak transcription	NHDF-Ad	bronchial

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