Variant report

Variant	rs12525342
Chromosome Location	chr6:25460678-25460679
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	chr6:25457887..25461292-chr6:25461516..25464637,3	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1028885	0.81[CHB][hapmap]
rs10498726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16890640	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35330592	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41271813	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41368745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6900224	0.81[CHB][hapmap]
rs73734011	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73734013	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7454031	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs969645	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12525342	HIST1H2BF	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25418800-25462600	Weak transcription	Ovary	ovary
2	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:25443200-25472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:25446800-25493600	Weak transcription	Left Ventricle	heart
7	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
8	chr6:25447400-25473200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:25448200-25472600	Weak transcription	Pancreas	Pancrea
10	chr6:25448400-25464400	Weak transcription	Thymus	Thymus
11	chr6:25449000-25462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:25449000-25463600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:25449400-25515800	Weak transcription	Lung	lung
14	chr6:25449600-25461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:25450400-25488400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:25450800-25461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:25450800-25462600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:25451600-25461000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:25451600-25461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:25452200-25473000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:25452400-25476000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:25452800-25467400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:25454200-25472800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:25454600-25462400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:25454800-25463600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:25455800-25460800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:25455800-25476000	Weak transcription	Aorta	Aorta
28	chr6:25456400-25462400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:25456400-25499200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:25456400-25515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
32	chr6:25458000-25461400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:25459000-25473000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:25459200-25463600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr6:25459400-25462800	Weak transcription	NH-A	brain
36	chr6:25459600-25465000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:25459800-25461000	Enhancers	Fetal Kidney	kidney
38	chr6:25459800-25471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:25460000-25460800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:25460000-25460800	Enhancers	Fetal Lung	lung
41	chr6:25460000-25464400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:25460000-25467600	Strong transcription	Primary T cells from cord blood	blood
43	chr6:25460200-25472000	Weak transcription	HMEC	breast
44	chr6:25460200-25476000	Weak transcription	NHEK	skin
45	chr6:25460400-25464400	Weak transcription	Fetal Thymus	thymus

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