Variant report

Variant	rs17022908
Chromosome Location	chr2:38783058-38783059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38780413..38785333-chr2:38976910..38979938,6	K562	blood:
2	chr2:38782046..38785023-chr2:38977532..38979938,4	K562	blood:
3	chr2:38773369..38778839-chr2:38780028..38785171,8	K562	blood:
4	chr2:38783037..38784703-chr2:38789757..38791472,2	K562	blood:
5	chr2:38781681..38785973-chr2:38793517..38796311,3	K562	blood:
6	chr2:38782788..38784491-chr2:38951489..38953190,2	K562	blood:
7	chr2:38781921..38784416-chr2:38785346..38789078,4	K562	blood:
8	chr2:38780198..38783785-chr2:38971693..38974497,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10201261	1.00[ASN][1000 genomes]
rs12328034	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13427352	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17022876	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs17022893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17022951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17022999	1.00[EUR][1000 genomes]
rs2278359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55992451	0.92[EUR][1000 genomes]
rs56131922	0.82[EUR][1000 genomes]
rs58563643	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59036182	1.00[EUR][1000 genomes]
rs6706212	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6751824	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs72907944	1.00[EUR][1000 genomes]
rs72909820	1.00[EUR][1000 genomes]
rs73930139	0.92[EUR][1000 genomes]
rs73931608	1.00[EUR][1000 genomes]
rs7566216	1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7581419	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586285	0.82[EUR][1000 genomes]
rs7594594	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17022908	STIP1	trans	brain	seeQTL
rs17022908	DEDD2	trans	brain	seeQTL
rs17022908	PLOD3	trans	brain	seeQTL
rs17022908	SPR	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:38770400-38786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
14	chr2:38770400-38787200	Weak transcription	NHLF	lung
15	chr2:38770400-38787200	Weak transcription	Osteobl	bone
16	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:38770600-38785800	Weak transcription	NH-A	brain
21	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:38770600-38794800	Weak transcription	NHEK	skin
23	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:38771000-38786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:38771200-38787200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel
27	chr2:38772800-38787400	Weak transcription	HepG2	liver
28	chr2:38775200-38783600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:38776400-38787400	Weak transcription	Fetal Kidney	kidney
31	chr2:38776600-38787200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:38776600-38787400	Weak transcription	Placenta	Placenta
33	chr2:38776600-38788000	Weak transcription	Brain Germinal Matrix	brain
34	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:38776800-38785200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:38776800-38787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:38776800-38787200	Weak transcription	Fetal Lung	lung
38	chr2:38776800-38787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:38776800-38788800	Weak transcription	Fetal Brain Male	brain
40	chr2:38777000-38787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
42	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:38777200-38787200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:38777200-38794200	Weak transcription	Ovary	ovary
45	chr2:38777400-38792600	Weak transcription	Thymus	Thymus
46	chr2:38777600-38787200	Weak transcription	A549	lung
47	chr2:38777600-38787400	Weak transcription	HMEC	breast
48	chr2:38778000-38784800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:38778200-38787200	Weak transcription	Left Ventricle	heart
50	chr2:38778200-38791400	Weak transcription	Fetal Intestine Small	intestine

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