Variant report

Variant	rs1699102
Chromosome Location	chr11:121456962-121456963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:121456678-121457211	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120975216..120977193-chr11:121456635..121459591,2	K562	blood:

Variant related genes	Relation type
SORL1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1010157	0.85[CEU][hapmap]
rs1010158	0.82[CEU][hapmap]
rs10892758	0.95[CEU][hapmap]
rs10892759	0.83[CEU][hapmap]
rs1503415	0.82[CEU][hapmap]
rs1503422	0.83[CEU][hapmap]
rs1625828	0.83[CEU][hapmap]
rs1792113	0.83[CEU][hapmap]
rs2282648	0.82[CEU][hapmap]
rs3824968	0.82[CEU][hapmap]
rs556349	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs726601	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1699102	GRIK4	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121407200-121459000	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:121416600-121471800	Strong transcription	Primary T cells from cord blood	blood
3	chr11:121431000-121466400	Weak transcription	Ovary	ovary
4	chr11:121435200-121464800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:121440600-121485000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:121443400-121464600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:121443800-121458600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:121443800-121461600	Weak transcription	Pancreas	Pancrea
9	chr11:121448400-121461200	Weak transcription	Gastric	stomach
10	chr11:121448800-121495600	Weak transcription	Stomach Mucosa	stomach
11	chr11:121449600-121457200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:121449800-121465800	Weak transcription	Adipose Nuclei	Adipose
13	chr11:121450000-121460200	Weak transcription	Brain Germinal Matrix	brain
14	chr11:121450200-121458600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:121450200-121460800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:121450200-121461600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:121450200-121461800	Weak transcription	Fetal Brain Male	brain
18	chr11:121450600-121460600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:121451000-121457800	Weak transcription	Fetal Lung	lung
20	chr11:121451000-121462600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:121451200-121461600	Weak transcription	Fetal Kidney	kidney
22	chr11:121451200-121464000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:121451200-121488200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:121451400-121459000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:121451400-121469600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr11:121451400-121470000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:121451600-121458400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:121451800-121457000	Genic enhancers	Fetal Thymus	thymus
29	chr11:121452000-121460000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:121452000-121466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:121453000-121460200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:121453000-121470800	Strong transcription	HepG2	liver
33	chr11:121453200-121459400	Weak transcription	Left Ventricle	heart
34	chr11:121453200-121504200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr11:121453400-121458000	Weak transcription	Brain Angular Gyrus	brain
36	chr11:121453400-121458400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:121453400-121458600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr11:121453400-121462000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:121453400-121491200	Weak transcription	Small Intestine	intestine
40	chr11:121453400-121505400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:121453600-121462000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:121453600-121469800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:121453800-121465800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:121454000-121503800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:121454200-121461200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:121454400-121457600	Weak transcription	Fetal Stomach	stomach
47	chr11:121454400-121458000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:121454400-121458000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:121454400-121458600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:121454400-121459800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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