Variant report

Variant	rs301396
Chromosome Location	chr6:25466889-25466890
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	chr6:25466796..25469622-chr6:25470987..25473848,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1752776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419563	0.92[ASN][1000 genomes]
rs435596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs463121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6910405	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467520	1.00[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs301396	HIST1H4E	cis	parietal	SCAN
rs301396	ZKSCAN4	cis	parietal	SCAN
rs301396	HIST1H2BB	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25433400-25472600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:25436200-25481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:25438200-25472600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:25443200-25472600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:25446800-25493600	Weak transcription	Left Ventricle	heart
6	chr6:25446800-25504400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:25447400-25473200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:25448200-25472600	Weak transcription	Pancreas	Pancrea
9	chr6:25449400-25515800	Weak transcription	Lung	lung
10	chr6:25450400-25488400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:25452200-25473000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:25452400-25476000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:25452800-25467400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:25454200-25472800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:25455800-25476000	Weak transcription	Aorta	Aorta
16	chr6:25456400-25499200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:25456400-25515800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
19	chr6:25459000-25473000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:25459800-25471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25460000-25467600	Strong transcription	Primary T cells from cord blood	blood
22	chr6:25460200-25472000	Weak transcription	HMEC	breast
23	chr6:25460200-25476000	Weak transcription	NHEK	skin
24	chr6:25461800-25469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:25462800-25477600	Weak transcription	Brain Anterior Caudate	brain
26	chr6:25463000-25472600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:25463000-25474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25463000-25476000	Weak transcription	HSMMtube	muscle
29	chr6:25463000-25490000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:25463200-25473000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:25463200-25481200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:25463800-25467000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:25463800-25487400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:25464000-25467800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:25464000-25498800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:25464200-25518400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:25464600-25473000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:25464800-25472600	Weak transcription	Fetal Thymus	thymus
40	chr6:25464800-25472600	Weak transcription	Thymus	Thymus
41	chr6:25464800-25475000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:25464800-25490000	Weak transcription	Hela-S3	cervix
43	chr6:25465000-25482800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:25465200-25472800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:25465200-25476200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:25465400-25470600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:25465400-25472600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:25465400-25472800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:25465400-25476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:25465400-25499000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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