Variant report

Variant	rs392230
Chromosome Location	chr6:28504639-28504640
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	chr6:28091278..28094202-chr6:28503615..28506105,2	K562	blood:
2	chr6:28498885..28501651-chr6:28502273..28504670,3	K562	blood:

Variant related genes	Relation type
ENSG00000196812	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10738069	0.83[ASN][1000 genomes]
rs10807039	0.82[ASN][1000 genomes]
rs16894139	1.00[ASW][hapmap]
rs16894166	0.90[EUR][1000 genomes]
rs2078035	0.82[AMR][1000 genomes]
rs2078439	0.82[AMR][1000 genomes]
rs2143766	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273106	0.82[AMR][1000 genomes]
rs28382604	0.82[AMR][1000 genomes]
rs377514	0.82[AMR][1000 genomes]
rs380879	0.86[AMR][1000 genomes]
rs389118	0.91[ASN][1000 genomes]
rs393414	0.87[ASN][1000 genomes]
rs437691	0.87[ASN][1000 genomes]
rs448450	0.86[AMR][1000 genomes]
rs454182	0.87[ASN][1000 genomes]
rs62402378	0.92[EUR][1000 genomes]
rs6456824	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6942252	0.92[EUR][1000 genomes]
rs72850099	0.88[EUR][1000 genomes]
rs732395	0.83[ASN][1000 genomes]
rs7748225	0.83[ASN][1000 genomes]
rs7760867	0.83[ASN][1000 genomes]
rs9468385	1.00[ASW][hapmap];0.84[CHD][hapmap];0.94[GIH][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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs392230	HIST1H2AE	cis	parietal	SCAN
rs392230	HIST1H2BB	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28504000-28509800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:28504200-28504800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:28504200-28505800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:28504400-28505600	Weak transcription	K562	blood
5	chr6:28504400-28506000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:28504400-28506200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:28504600-28504800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr6:28504600-28504800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr6:28504600-28504800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:28504600-28504800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:28504600-28504800	Active TSS	Fetal Brain Female	brain
12	chr6:28504600-28505200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:28504600-28505200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:28504600-28505200	Active TSS	Fetal Stomach	stomach
15	chr6:28504600-28505400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:28504600-28505400	Active TSS	Brain Germinal Matrix	brain
17	chr6:28504600-28505400	Active TSS	HUVEC	blood vessel
18	chr6:28504600-28505400	Active TSS	NH-A	brain
19	chr6:28504600-28505600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:28504600-28505600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr6:28504600-28505600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:28504600-28505800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:28504600-28505800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:28504600-28505800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:28504600-28506000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr6:28504600-28506000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:28504600-28506000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:28504600-28506000	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr6:28504600-28506000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:28504600-28506000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:28504600-28506000	Active TSS	GM12878-XiMat	blood
32	chr6:28504600-28506200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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