Variant report

Variant	rs2018839
Chromosome Location	chr6:25300739-25300740
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	chr6:25290098..25292506-chr6:25299738..25301945,2	MCF-7	breast:
2	chr6:25278449..25281272-chr6:25299737..25301781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10456320	0.83[LWK][hapmap]
rs2064206	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143022	0.80[CEU][hapmap]
rs2690041	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2690110	0.85[JPT][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap]
rs2690117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690118	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2690132	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690134	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2690135	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744288	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744289	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744293	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744294	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744297	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744299	0.80[CEU][hapmap]
rs2744300	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914799	0.82[CHD][hapmap]
rs6926126	0.82[CHD][hapmap]
rs7752524	1.00[LWK][hapmap]
rs7764258	0.94[LWK][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2018839	HIST1H3G	cis	parietal	SCAN
rs2018839	HIST1H3B	cis	cerebellum	SCAN
rs2018839	TRIM38	cis	cerebellum	SCAN
rs2018839	SLC17A1	cis	parietal	SCAN

Chromatin state (count:71 , 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	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
4	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:25292400-25301000	Weak transcription	Adipose Nuclei	Adipose
7	chr6:25293000-25301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:25293200-25301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:25294200-25311200	Weak transcription	Lung	lung
10	chr6:25294600-25301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:25296000-25301200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:25296400-25302400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:25296600-25301200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:25296600-25302400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:25296600-25302600	Weak transcription	Colonic Mucosa	Colon
16	chr6:25296800-25301800	Weak transcription	Fetal Intestine Large	intestine
17	chr6:25296800-25302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:25297200-25302600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:25297200-25303200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:25297400-25300800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:25297400-25301600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:25297400-25301800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:25297400-25302400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:25297400-25303000	Weak transcription	Gastric	stomach
25	chr6:25297400-25304600	Weak transcription	Left Ventricle	heart
26	chr6:25297600-25300800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:25297600-25301800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:25297800-25301200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:25297800-25301200	Weak transcription	Brain Angular Gyrus	brain
30	chr6:25297800-25301200	Weak transcription	Fetal Thymus	thymus
31	chr6:25297800-25301200	Weak transcription	Thymus	Thymus
32	chr6:25297800-25302400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:25298000-25300800	Weak transcription	Small Intestine	intestine
34	chr6:25298000-25301200	Weak transcription	Fetal Intestine Small	intestine
35	chr6:25298000-25301400	Weak transcription	NHDF-Ad	bronchial
36	chr6:25298000-25301800	Weak transcription	Stomach Mucosa	stomach
37	chr6:25298000-25302400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:25298000-25302400	Weak transcription	Ovary	ovary
39	chr6:25298000-25302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:25298000-25302800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:25298000-25303200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:25298200-25300800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:25298200-25301000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:25298200-25301200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:25298200-25303000	Weak transcription	Fetal Kidney	kidney
47	chr6:25298400-25302600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:25298600-25303000	Enhancers	Aorta	Aorta
49	chr6:25298600-25303400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr6:25298800-25302000	Weak transcription	Fetal Heart	heart

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