Variant report

Variant	rs9295928
Chromosome Location	chr6:30823630-30823631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30823525..30825673-chr6:30833056..30834672,2	K562	blood:
2	chr6:30582957..30586155-chr6:30822684..30826202,3	K562	blood:

Variant related genes	Relation type
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204568	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10947113	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947114	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528271	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12697941	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074511	0.92[EUR][1000 genomes]
rs2239518	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2240803	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2267641	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285319	0.86[EUR][1000 genomes]
rs2286655	0.92[EUR][1000 genomes]
rs2286656	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2524236	0.85[EUR][1000 genomes]
rs3213644	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3916232	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711247	0.86[EUR][1000 genomes]
rs4711249	0.92[EUR][1000 genomes]
rs4713402	0.92[EUR][1000 genomes]
rs9295930	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295933	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9366761	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368646	0.92[EUR][1000 genomes]
rs9394021	0.86[EUR][1000 genomes]
rs9461639	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468841	0.86[AMR][1000 genomes]
rs9468843	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468847	0.92[EUR][1000 genomes]
rs9501030	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9501035	0.92[EUR][1000 genomes]
rs9501340	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501491	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884108	chr6:30821187-30838497	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9295928	HIST1H2AM	cis	cerebellum	SCAN
rs9295928	VARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30816200-30824600	Weak transcription	Fetal Kidney	kidney
2	chr6:30820600-30824800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:30820600-30825000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:30821600-30825000	Enhancers	Placenta	Placenta
5	chr6:30822400-30823800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:30822800-30825200	Enhancers	Fetal Intestine Large	intestine
7	chr6:30823200-30823800	Flanking Active TSS	HepG2	liver
8	chr6:30823200-30824000	Enhancers	Duodenum Mucosa	Duodenum
9	chr6:30823200-30824400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr6:30823200-30825200	Enhancers	Fetal Intestine Small	intestine
11	chr6:30823200-30826400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:30823400-30824000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:30823400-30824200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:30823400-30825400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:30823600-30824000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr6:30823600-30826400	Enhancers	Fetal Thymus	thymus
17	chr6:30823600-30835400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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