Variant report

Variant	rs10892759
Chromosome Location	chr11:121464088-121464089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1010158	0.81[GIH][hapmap]
rs1010159	0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs10892758	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503423	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1619545	0.80[EUR][1000 genomes]
rs1620003	0.83[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1625828	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1629493	0.80[GIH][hapmap]
rs1699102	0.83[CEU][hapmap]
rs1699103	0.81[CEU][hapmap]
rs1699108	0.80[CEU][hapmap]
rs1784931	0.83[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap]
rs1790213	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1792113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792122	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792125	0.81[CEU][hapmap]
rs556349	0.83[CEU][hapmap]
rs639648	0.80[CEU][hapmap]
rs640479	0.81[CEU][hapmap]

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	nsv975233	chr11:121359656-121574786	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv527072	chr11:121448090-121486552	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv34768	chr11:121452651-121534938	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10892759	SC5DL	cis	cerebellum	SCAN
rs10892759	GRIK4	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121416600-121471800	Strong transcription	Primary T cells from cord blood	blood
2	chr11:121431000-121466400	Weak transcription	Ovary	ovary
3	chr11:121435200-121464800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:121440600-121485000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:121443400-121464600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:121448800-121495600	Weak transcription	Stomach Mucosa	stomach
7	chr11:121449800-121465800	Weak transcription	Adipose Nuclei	Adipose
8	chr11:121451200-121488200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr11:121451400-121469600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:121451400-121470000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:121452000-121466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:121453000-121470800	Strong transcription	HepG2	liver
13	chr11:121453200-121504200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:121453400-121491200	Weak transcription	Small Intestine	intestine
15	chr11:121453400-121505400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:121453600-121469800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:121453800-121465800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:121454000-121503800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:121454400-121469600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr11:121454400-121504000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr11:121454800-121503600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:121455600-121503800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:121455800-121469800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:121456400-121465600	Strong transcription	NHEK	skin
25	chr11:121456600-121469600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:121456600-121471400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:121456600-121501200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:121456800-121464600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr11:121458000-121495000	Weak transcription	Right Ventricle	heart
30	chr11:121458800-121469000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:121459000-121469600	Strong transcription	Fetal Intestine Large	intestine
32	chr11:121459200-121501400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr11:121459400-121467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:121459600-121464400	Strong transcription	HMEC	breast
35	chr11:121459800-121464600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
36	chr11:121460200-121464400	Genic enhancers	Liver	Liver
37	chr11:121460400-121466000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:121460400-121491800	Weak transcription	Left Ventricle	heart
39	chr11:121460800-121467000	Weak transcription	Aorta	Aorta
40	chr11:121461000-121491200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:121461400-121506200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:121461800-121471200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:121461800-121505400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:121462000-121465800	Weak transcription	Colonic Mucosa	Colon
45	chr11:121462000-121466000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:121462000-121466000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:121462200-121466000	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:121462200-121466000	Weak transcription	Gastric	stomach
49	chr11:121462200-121466400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr11:121462200-121466400	Weak transcription	Esophagus	oesophagus

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