Variant report

Variant	rs10456320
Chromosome Location	chr6:25292401-25292402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25279474..25282402-chr6:25292277..25293870,2	MCF-7	breast:
2	chr6:25290098..25292506-chr6:25299738..25301945,2	MCF-7	breast:
3	chr6:25278861..25280668-chr6:25291902..25293874,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCGN-5	chr6:25292177-25292436	NONHSAT108151

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2018839	0.83[LWK][hapmap]
rs4712910	0.85[YRI][hapmap]
rs6902634	1.00[YRI][hapmap]
rs7743997	1.00[YRI][hapmap]
rs7752524	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs7764258	0.83[LWK][hapmap];1.00[YRI][hapmap]
rs7767189	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10456320	HIST1H3C	cis	parietal	SCAN
rs10456320	PRRX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25281200-25293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:25281600-25293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:25281600-25293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:25281600-25294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
14	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
16	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:25281800-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:25282200-25293800	Weak transcription	Lung	lung
19	chr6:25282800-25296400	Weak transcription	Hela-S3	cervix
20	chr6:25286400-25295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:25287800-25296000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:25288400-25293600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:25288600-25292600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:25288600-25295400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:25288600-25296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:25288600-25296400	Weak transcription	Gastric	stomach
28	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
29	chr6:25289000-25295800	Weak transcription	Esophagus	oesophagus
30	chr6:25289000-25298600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:25289000-25300600	Weak transcription	Pancreas	Pancrea
32	chr6:25290200-25292800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:25290600-25293200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr6:25290800-25292800	Weak transcription	Ovary	ovary
36	chr6:25290800-25294200	Weak transcription	Aorta	Aorta
37	chr6:25291000-25293200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:25291000-25295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:25291000-25296000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:25291000-25296000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:25291200-25292600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:25291200-25295800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:25291200-25295800	Weak transcription	Fetal Intestine Large	intestine
44	chr6:25291200-25295800	Weak transcription	Right Atrium	heart
45	chr6:25291200-25296400	Weak transcription	Left Ventricle	heart
46	chr6:25291600-25292600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:25291800-25293200	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr6:25291800-25296600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:25292000-25292600	Enhancers	Fetal Lung	lung
50	chr6:25292000-25293000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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