Variant report

Variant	rs7080894
Chromosome Location	chr10:99517848-99517849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10748708	0.90[ASN][1000 genomes]
rs10748709	0.87[ASN][1000 genomes]
rs10786367	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs10786370	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs10786371	0.84[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10786372	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs10786373	0.88[ASN][1000 genomes]
rs10882993	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10882995	0.84[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.82[ASN][1000 genomes]
rs10882996	0.81[ASN][1000 genomes]
rs10882997	0.86[ASN][1000 genomes]
rs10882998	0.91[CHB][hapmap]
rs11189353	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11189355	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs11189356	0.81[ASN][1000 genomes]
rs11189357	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11189359	0.84[CHD][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];0.82[ASN][1000 genomes]
rs11189360	0.85[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs11189361	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11189362	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11591898	0.81[ASN][1000 genomes]
rs12412543	0.81[ASN][1000 genomes]
rs12569711	0.81[ASN][1000 genomes]
rs12783992	0.87[ASN][1000 genomes]
rs1538723	0.82[ASN][1000 genomes]
rs1556971	0.89[ASN][1000 genomes]
rs1981237	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1981238	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2010732	0.81[ASN][1000 genomes]
rs2027376	0.94[ASN][1000 genomes]
rs2039826	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs34283185	0.86[ASN][1000 genomes]
rs3750612	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs3750614	0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3750615	0.81[JPT][hapmap]
rs3814558	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3814559	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3814560	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4244329	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4917784	0.82[JPT][hapmap]
rs4917786	0.84[ASN][1000 genomes]
rs4919139	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs7072751	0.86[ASN][1000 genomes]
rs7077725	0.82[ASN][1000 genomes]
rs7080953	1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7081652	0.89[ASN][1000 genomes]
rs7094519	0.81[ASN][1000 genomes]
rs7099540	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7907679	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7910589	0.87[ASN][1000 genomes]
rs7916164	0.93[ASN][1000 genomes]
rs7916454	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7916593	0.94[ASN][1000 genomes]
rs7922907	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs883324	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs946777	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs946778	0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7080894	ZFYVE27	cis	cerebellum	SCAN
rs7080894	C10orf12	cis	cerebellum	SCAN
rs7080894	ZFYVE27	cis	parietal	SCAN
rs7080894	UBTD1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99497600-99522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:99498200-99520600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:99498400-99519000	Strong transcription	Fetal Intestine Large	intestine
4	chr10:99498400-99519200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr10:99498600-99518000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:99498600-99518000	Strong transcription	Fetal Thymus	thymus
7	chr10:99498600-99520200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99498600-99520600	Strong transcription	Osteobl	bone
9	chr10:99498600-99522200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr10:99498600-99522400	Strong transcription	Duodenum Mucosa	Duodenum
11	chr10:99498600-99522400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr10:99498600-99523000	Strong transcription	Thymus	Thymus
13	chr10:99498600-99523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:99498600-99524800	Weak transcription	Fetal Brain Male	brain
15	chr10:99498800-99522400	Strong transcription	Dnd41	blood
16	chr10:99499000-99518000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:99499200-99518000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:99499200-99522800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr10:99499200-99523400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:99499400-99519000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:99499400-99522000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr10:99499400-99522400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:99499600-99519200	Strong transcription	Placenta	Placenta
24	chr10:99499800-99518000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr10:99500000-99523000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr10:99500200-99518000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:99500400-99522000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:99500600-99523200	Strong transcription	Brain Germinal Matrix	brain
29	chr10:99500800-99518800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:99502000-99518000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:99502000-99522800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr10:99502200-99522600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:99502400-99520000	Strong transcription	Primary B cells from cord blood	blood
34	chr10:99502600-99518000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:99502600-99519200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:99502600-99522600	Strong transcription	Primary T cells from cord blood	blood
37	chr10:99502800-99518000	Strong transcription	A549	lung
38	chr10:99502800-99521600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:99502800-99522600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:99503000-99524000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:99503200-99519000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr10:99503400-99518000	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr10:99503400-99522200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:99503400-99522800	Strong transcription	Liver	Liver
45	chr10:99503600-99519200	Strong transcription	Adipose Nuclei	Adipose
46	chr10:99503600-99522400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr10:99504000-99520600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:99504200-99521800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:99504200-99523600	Strong transcription	Fetal Intestine Small	intestine
50	chr10:99504600-99522000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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