Variant report

Variant	rs10807297
Chromosome Location	chr6:44278592-44278593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44214136..44216298-chr6:44277914..44280865,2	MCF-7	breast:
2	chr6:44213575..44218708-chr6:44278177..44283526,11	K562	blood:
3	chr6:44234588..44237594-chr6:44277478..44280850,3	MCF-7	breast:
4	chr6:44213056..44218708-chr6:44277561..44284910,14	K562	blood:
5	chr6:44216338..44218124-chr6:44278260..44280536,2	MCF-7	breast:
6	chr6:44231603..44235224-chr6:44277267..44282023,5	MCF-7	breast:
7	chr6:44261562..44267016-chr6:44278207..44281216,9	MCF-7	breast:
8	chr6:44222000..44226440-chr6:44278583..44281839,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146232	Chromatin interaction
ENSG00000146221	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000096384	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1123523	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205227	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12215176	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12664825	0.87[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12943	0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2297335	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297336	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs324138	0.89[ASN][1000 genomes]
rs324139	0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs324140	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs324142	0.90[ASN][1000 genomes]
rs324144	0.90[ASN][1000 genomes]
rs324145	0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs324146	0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs324147	0.90[ASN][1000 genomes]
rs325017	0.89[ASN][1000 genomes]
rs325018	0.89[ASN][1000 genomes]
rs325019	0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.83[ASN][1000 genomes]
rs34865422	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4714774	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs516582	0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs524533	0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[MKK][hapmap]
rs529948	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs545970	0.90[JPT][hapmap]
rs551145	0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap]
rs557373	0.90[ASN][1000 genomes]
rs570469	0.89[ASN][1000 genomes]
rs571770	0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[MKK][hapmap]
rs614715	0.90[ASN][1000 genomes]
rs694349	0.89[ASN][1000 genomes]
rs844315	0.87[ASN][1000 genomes]
rs9369469	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9381305	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9381306	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9381307	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9381308	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394999	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395000	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9395001	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10807297	PLA2G7	cis	cerebellum	SCAN
rs10807297	ENPP5	cis	parietal	SCAN
rs10807297	HSP90AB1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44265600-44279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:44266000-44280000	Weak transcription	Small Intestine	intestine
3	chr6:44266200-44279600	Weak transcription	Right Atrium	heart
4	chr6:44266800-44279200	Strong transcription	Brain Cingulate Gyrus	brain
5	chr6:44266800-44279800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:44267000-44279600	Strong transcription	Fetal Muscle Leg	muscle
7	chr6:44267000-44279800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:44267000-44279800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr6:44267200-44279400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:44267200-44279600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:44267200-44279600	Strong transcription	Fetal Thymus	thymus
12	chr6:44267200-44279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:44267200-44279800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:44267400-44279200	Strong transcription	Liver	Liver
15	chr6:44267400-44279400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:44267400-44279600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:44267400-44279600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:44267400-44280000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:44267400-44280000	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr6:44267600-44279200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr6:44267600-44279400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr6:44267600-44279800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:44267800-44279800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:44267800-44279800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr6:44268000-44278800	Strong transcription	Dnd41	blood
26	chr6:44268000-44279200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:44268000-44279200	Strong transcription	Fetal Brain Female	brain
28	chr6:44268000-44279200	Strong transcription	Gastric	stomach
29	chr6:44268000-44279200	Strong transcription	HepG2	liver
30	chr6:44268000-44279400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:44268000-44279400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:44268000-44279400	Strong transcription	Primary T cells from cord blood	blood
33	chr6:44268000-44279400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:44268000-44279400	Strong transcription	Brain Hippocampus Middle	brain
35	chr6:44268000-44279600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:44268000-44279600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:44268000-44279600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:44268000-44279600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:44268000-44279600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:44268000-44279600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:44268000-44279600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr6:44268000-44279600	Strong transcription	Adipose Nuclei	Adipose
43	chr6:44268000-44279600	Strong transcription	Brain Angular Gyrus	brain
44	chr6:44268000-44279600	Strong transcription	Brain Anterior Caudate	brain
45	chr6:44268000-44279600	Strong transcription	Brain Germinal Matrix	brain
46	chr6:44268000-44279600	Strong transcription	Ovary	ovary
47	chr6:44268000-44279600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr6:44268000-44279800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:44268000-44279800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr6:44268000-44279800	Strong transcription	Primary B cells from peripheral blood	blood

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