Variant report

Variant	rs17027886
Chromosome Location	chr4:99565938-99565939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99565530..99567137-chr4:99836060..99837729,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10489126	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10516435	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17027883	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41399047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6829297	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6831674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7685150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7699492	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[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs883510	0.92[ASN][1000 genomes]

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	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17027886	ADH1A	cis	cerebellum	SCAN
rs17027886	EIF4E	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99548000-99569200	Weak transcription	Gastric	stomach
2	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
3	chr4:99552600-99569600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:99552800-99569200	Weak transcription	Fetal Stomach	stomach
5	chr4:99554200-99569200	Weak transcription	Spleen	Spleen
6	chr4:99560200-99569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:99560600-99568000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:99560800-99566400	Weak transcription	Brain Germinal Matrix	brain
9	chr4:99560800-99568200	Weak transcription	Fetal Lung	lung
10	chr4:99561000-99566000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:99561200-99567000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:99561200-99567200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:99562000-99566000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:99562000-99569200	Weak transcription	Fetal Brain Male	brain
15	chr4:99563200-99566400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr4:99563400-99566000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:99563400-99566600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:99563400-99567000	Weak transcription	Stomach Mucosa	stomach
19	chr4:99563600-99566600	Enhancers	HUVEC	blood vessel
20	chr4:99563800-99566000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr4:99564000-99566600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:99564000-99567200	Enhancers	Brain Angular Gyrus	brain
23	chr4:99564000-99571600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr4:99564200-99566200	Enhancers	Fetal Thymus	thymus
25	chr4:99564200-99568400	Enhancers	Thymus	Thymus
26	chr4:99564200-99569200	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:99564200-99570400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:99564400-99575600	Weak transcription	Fetal Kidney	kidney
29	chr4:99564600-99566800	Enhancers	NH-A	brain
30	chr4:99564600-99569400	Weak transcription	Fetal Heart	heart
31	chr4:99564800-99566000	Enhancers	Primary T cells from cord blood	blood
32	chr4:99564800-99566000	Enhancers	Primary T cells fromperipheralblood	blood
33	chr4:99564800-99566200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr4:99564800-99566200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:99564800-99568400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:99564800-99568400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:99565000-99566000	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:99565000-99566800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:99565200-99566000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:99565200-99566800	Weak transcription	Ovary	ovary
41	chr4:99565200-99567000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:99565200-99567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:99565200-99568000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:99565200-99568200	Weak transcription	Fetal Brain Female	brain
45	chr4:99565200-99568200	Weak transcription	Osteobl	bone
46	chr4:99565200-99568400	Weak transcription	HSMM	muscle
47	chr4:99565200-99568600	Weak transcription	HSMMtube	muscle
48	chr4:99565200-99569200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:99565200-99569200	Weak transcription	NHLF	lung
50	chr4:99565200-99569400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links