Variant report

Variant	rs9380607
Chromosome Location	chr6:36796133-36796134
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36795450..36797184-chr6:36798475..36800268,2	MCF-7	breast:
2	chr6:36794334..36796730-chr6:36804291..36808430,4	K562	blood:
3	chr6:36735205..36738039-chr6:36795328..36797807,2	K562	blood:
4	chr6:36785208..36787449-chr6:36793356..36796337,2	K562	blood:
5	chr6:36794960..36797017-chr6:36818260..36820420,2	MCF-7	breast:
6	chr6:36795234..36797828-chr6:36799282..36801814,2	MCF-7	breast:
7	chr6:36789119..36791202-chr6:36794316..36796954,2	MCF-7	breast:
8	chr6:36794979..36796750-chr6:36806807..36808819,2	K562	blood:
9	chr6:36777747..36780393-chr6:36794218..36796370,2	K562	blood:
10	chr6:36561261..36563534-chr6:36794146..36796265,2	K562	blood:
11	chr6:36794469..36796279-chr6:36812712..36815459,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000124772	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11751790	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11751844	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11754437	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11756425	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11758600	0.89[AFR][1000 genomes]
rs11758807	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661551	0.89[AFR][1000 genomes]
rs2007290	0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs2071822	0.82[ASW][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2071823	0.82[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2293381	1.00[YRI][hapmap]
rs236381	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs28656041	0.96[ASN][1000 genomes]
rs28673271	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3176344	1.00[YRI][hapmap]
rs3213536	1.00[YRI][hapmap]
rs4711470	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711472	0.89[AFR][1000 genomes]
rs4714015	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4714019	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs60097056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62406642	0.89[AFR][1000 genomes]
rs62406644	0.89[AFR][1000 genomes]
rs6910582	0.89[AFR][1000 genomes]
rs6912602	0.85[GIH][hapmap];0.90[TSI][hapmap]
rs6913047	0.89[AFR][1000 genomes]
rs72846083	0.89[AFR][1000 genomes]
rs7745099	0.85[GIH][hapmap]
rs9349015	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9368961	0.96[ASN][1000 genomes]
rs9368963	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9368964	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368965	0.82[ASW][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9380603	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9380605	0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9380614	0.82[ASW][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9394387	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5261	chr6:36754545-36798824	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9380607	C6orf89	cis	cerebellum	SCAN
rs9380607	C6orf64	cis	parietal	SCAN
rs9380607	C6orf125	cis	parietal	SCAN
rs9380607	MTCH1	cis	parietal	SCAN
rs9380607	LRFN2	cis	cerebellum	SCAN
rs9380607	C6orf89	cis	parietal	SCAN
rs9380607	SCUBE3	cis	parietal	SCAN
rs9380607	TCP11	cis	cerebellum	SCAN
rs9380607	MAPK13	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36777000-36797800	Weak transcription	Pancreas	Pancrea
2	chr6:36779400-36797600	Weak transcription	Fetal Brain Female	brain
3	chr6:36787400-36796400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:36788400-36802400	Weak transcription	Fetal Kidney	kidney
5	chr6:36788800-36797200	Enhancers	Right Atrium	heart
6	chr6:36789200-36796400	Enhancers	Left Ventricle	heart
7	chr6:36789800-36802200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:36790600-36799400	Enhancers	Fetal Muscle Leg	muscle
9	chr6:36791200-36805800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:36791400-36798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:36791600-36797000	Enhancers	Right Ventricle	heart
12	chr6:36792000-36796200	Enhancers	Fetal Heart	heart
13	chr6:36792400-36796600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr6:36793400-36796600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:36793600-36796600	Enhancers	Adipose Nuclei	Adipose
16	chr6:36793800-36796200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:36793800-36796600	Enhancers	Brain Anterior Caudate	brain
18	chr6:36794000-36796400	Enhancers	Placenta	Placenta
19	chr6:36794000-36797200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:36794200-36796400	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:36794200-36796400	Enhancers	Brain Hippocampus Middle	brain
22	chr6:36794200-36796800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:36794400-36796200	Enhancers	NH-A	brain
24	chr6:36794400-36796800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:36794600-36796400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:36794600-36796600	Enhancers	Primary hematopoietic stem cells	blood
27	chr6:36794800-36796200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:36794800-36797200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:36794800-36797600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:36794800-36797600	Enhancers	HepG2	liver
31	chr6:36795000-36796200	Enhancers	Fetal Lung	lung
32	chr6:36795000-36796400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:36795000-36796400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:36795000-36796800	Enhancers	Fetal Thymus	thymus
35	chr6:36795000-36797800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:36795200-36797600	Weak transcription	Stomach Mucosa	stomach
37	chr6:36795200-36797800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:36795200-36798600	Enhancers	HUVEC	blood vessel
39	chr6:36795200-36802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:36795400-36796600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:36795400-36797600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:36795400-36797800	Weak transcription	Brain Substantia Nigra	brain
43	chr6:36795400-36798800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:36795600-36796600	Enhancers	Fetal Muscle Trunk	muscle
45	chr6:36795600-36797000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:36795600-36797600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr6:36795600-36797800	Weak transcription	Esophagus	oesophagus
48	chr6:36795600-36797800	Weak transcription	Lung	lung
49	chr6:36795600-36797800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr6:36795600-36798000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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