Variant report

Variant	rs10896299
Chromosome Location	chr11:67948544-67948545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10791958	0.84[JPT][hapmap]
rs10896298	0.82[CEU][hapmap]
rs10896300	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap]
rs11228151	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1540209	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2511477	1.00[JPT][hapmap]
rs4930561	0.82[CEU][hapmap]
rs6591334	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6591335	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7122250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7126326	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7945995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7946212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10896299	POLA2	cis	parietal	SCAN
rs10896299	SUV420H1	Cis_1M	lymphoblastoid	RTeQTL
rs10896299	CDC42BPG	cis	cerebellum	SCAN
rs10896299	SYT12	cis	cerebellum	SCAN
rs10896299	FLRT1	cis	cerebellum	SCAN
rs10896299	FGF19	cis	parietal	SCAN
rs10896299	RNASEH2C	cis	parietal	SCAN
rs10896299	SLC25A45	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67915000-67973800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:67922600-67956600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:67924200-67949800	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr11:67924400-67956600	Strong transcription	Fetal Intestine Large	intestine
5	chr11:67924400-67956800	Strong transcription	Primary T cells from cord blood	blood
6	chr11:67924400-67957000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:67924600-67956400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr11:67924600-67956600	Strong transcription	Fetal Muscle Leg	muscle
9	chr11:67925200-67955000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:67928000-67956600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr11:67928400-67950000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:67928600-67955400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:67928800-67954200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:67928800-67954600	Strong transcription	Dnd41	blood
15	chr11:67928800-67955200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:67929000-67954400	Strong transcription	Adipose Nuclei	Adipose
17	chr11:67929000-67955200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:67929000-67957600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:67929200-67956800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:67929200-67957600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:67929400-67953400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:67929600-67954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:67930000-67954000	Strong transcription	Placenta	Placenta
24	chr11:67930000-67955400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:67930400-67953200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:67930400-67954200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:67931200-67954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:67931400-67957600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:67932400-67954400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:67932400-67956800	Strong transcription	Fetal Thymus	thymus
31	chr11:67932800-67954200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:67934400-67955600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:67937000-67949600	Weak transcription	Fetal Heart	heart
34	chr11:67938200-67953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr11:67938200-67961200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:67938600-67960600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:67939200-67953200	Weak transcription	Small Intestine	intestine
38	chr11:67940200-67951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:67940400-67955600	Weak transcription	NHLF	lung
40	chr11:67941600-67949800	Weak transcription	Gastric	stomach
41	chr11:67941800-67958200	Weak transcription	Esophagus	oesophagus
42	chr11:67942000-67949200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:67942000-67951200	Weak transcription	HMEC	breast
44	chr11:67942000-67953000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:67942200-67951400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:67942200-67953200	Strong transcription	Liver	Liver
47	chr11:67942200-67954800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr11:67942200-67959600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:67942400-67949200	Weak transcription	Pancreas	Pancrea
50	chr11:67942400-67953600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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