Variant report

Variant	rs6574126
Chromosome Location	chr14:25474449-25474450
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:25474104..25476985-chr14:25480254..25482757,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10143606	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10147992	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs11159034	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs2004925	0.92[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2038700	0.82[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2332462	0.92[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7141943	0.92[ASW][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8017228	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs873102	0.85[CHD][hapmap];0.84[GIH][hapmap];0.88[MKK][hapmap]
rs912304	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6574126	RNF31	cis	parietal	SCAN
rs6574126	SNORD8	cis	cerebellum	SCAN
rs6574126	OR5AU1	cis	parietal	SCAN
rs6574126	STXBP6	cis	parietal	SCAN
rs6574126	REM2	cis	cerebellum	SCAN
rs6574126	SUPT16H	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25463200-25476600	Weak transcription	Placenta	Placenta
2	chr14:25468000-25476000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr14:25470600-25475600	Weak transcription	NH-A	brain
4	chr14:25470800-25475600	Weak transcription	Fetal Lung	lung
5	chr14:25470800-25475800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:25470800-25475800	Weak transcription	NHLF	lung
7	chr14:25471200-25476200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr14:25472200-25476200	Enhancers	HSMM	muscle
9	chr14:25472400-25474800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr14:25472400-25474800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr14:25472600-25474800	Enhancers	NHDF-Ad	bronchial
12	chr14:25473000-25476400	Weak transcription	Brain Anterior Caudate	brain
13	chr14:25473000-25477800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:25473200-25474800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr14:25473200-25476200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:25473400-25476600	Weak transcription	Adipose Nuclei	Adipose
17	chr14:25473400-25476600	Weak transcription	Fetal Muscle Leg	muscle
18	chr14:25473400-25477200	Enhancers	Fetal Intestine Small	intestine
19	chr14:25473400-25477800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:25473400-25478600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:25473400-25478800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:25473400-25479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr14:25473600-25475200	Weak transcription	HSMMtube	muscle
24	chr14:25473600-25475600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:25473600-25475800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:25473600-25475800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:25473600-25476200	Weak transcription	Brain Angular Gyrus	brain
28	chr14:25473600-25476200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr14:25473600-25476200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr14:25473600-25476400	Weak transcription	Brain Hippocampus Middle	brain
31	chr14:25473600-25478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr14:25473800-25475200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:25473800-25475400	Weak transcription	Fetal Heart	heart
34	chr14:25473800-25475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:25473800-25478000	Weak transcription	Fetal Brain Male	brain
36	chr14:25473800-25478200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:25474000-25475200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr14:25474200-25474800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr14:25474200-25475200	Weak transcription	Left Ventricle	heart
40	chr14:25474200-25475200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr14:25474200-25475400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr14:25474200-25475600	Weak transcription	Stomach Mucosa	stomach
43	chr14:25474200-25475800	Weak transcription	NHEK	skin
44	chr14:25474200-25475800	Weak transcription	Osteobl	bone
45	chr14:25474200-25476200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr14:25474200-25476600	Weak transcription	Pancreas	Pancrea
47	chr14:25474200-25476600	Weak transcription	Right Atrium	heart
48	chr14:25474200-25476600	Weak transcription	Right Ventricle	heart
49	chr14:25474200-25476800	Weak transcription	Brain Substantia Nigra	brain
50	chr14:25474200-25477800	Enhancers	HepG2	liver

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