Variant report

Variant	rs12168052
Chromosome Location	chr22:31440703-31440704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31439219..31443340-chr22:31479162..31482694,5	K562	blood:
2	chr22:31437736..31441147-chr22:31443914..31447179,4	K562	blood:

Variant related genes	Relation type
ENSG00000273387	Chromatin interaction
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12157450	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12165786	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12170984	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12330058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2006301	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2074738	0.88[CEU][hapmap]
rs5753434	0.83[GIH][hapmap]
rs5753436	0.85[GIH][hapmap]
rs5994366	1.00[JPT][hapmap]
rs5994370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs715297	1.00[JPT][hapmap]
rs7284593	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7285683	1.00[JPT][hapmap]
rs7291565	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs736901	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs9619164	0.95[EUR][1000 genomes]
rs9619167	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]

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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv966103	chr22:31410201-31452981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12168052	SEC14L4	cis	cerebellum	SCAN
rs12168052	SEZ6L	cis	cerebellum	SCAN
rs12168052	CABP7	cis	parietal	SCAN
rs12168052	LACTB2	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31433600-31441400	Weak transcription	Spleen	Spleen
2	chr22:31433600-31442200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:31433600-31442600	Weak transcription	HSMM	muscle
4	chr22:31433800-31446000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr22:31436000-31441400	Weak transcription	Colonic Mucosa	Colon
6	chr22:31436000-31441800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr22:31436000-31442200	Weak transcription	Placenta	Placenta
8	chr22:31439800-31441200	Enhancers	Fetal Stomach	stomach
9	chr22:31440000-31453200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr22:31440200-31440800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:31440200-31440800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:31440200-31440800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:31440200-31440800	Enhancers	Fetal Intestine Large	intestine
14	chr22:31440200-31440800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr22:31440200-31440800	Flanking Active TSS	HepG2	liver
16	chr22:31440200-31441000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr22:31440200-31441600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr22:31440200-31441800	Enhancers	Lung	lung
19	chr22:31440200-31442800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr22:31440200-31443000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr22:31440200-31443200	Enhancers	Fetal Muscle Trunk	muscle
22	chr22:31440200-31443400	Enhancers	Fetal Muscle Leg	muscle
23	chr22:31440200-31443400	Enhancers	Right Ventricle	heart
24	chr22:31440200-31443400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr22:31440200-31443600	Enhancers	Ovary	ovary
26	chr22:31440200-31443800	Enhancers	Left Ventricle	heart
27	chr22:31440200-31447400	Enhancers	Adipose Nuclei	Adipose
28	chr22:31440400-31440800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr22:31440400-31440800	Enhancers	NHDF-Ad	bronchial
30	chr22:31440400-31440800	Enhancers	NHLF	lung
31	chr22:31440400-31441000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:31440400-31441000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:31440400-31442000	Weak transcription	K562	blood
34	chr22:31440400-31443000	Enhancers	Rectal Smooth Muscle	rectum
35	chr22:31440600-31440800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:31440600-31440800	Enhancers	Brain Anterior Caudate	brain
37	chr22:31440600-31440800	Enhancers	Colon Smooth Muscle	Colon
38	chr22:31440600-31440800	Enhancers	Fetal Intestine Small	intestine
39	chr22:31440600-31441400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr22:31440600-31442000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr22:31440600-31442000	Weak transcription	Right Atrium	heart
42	chr22:31440600-31442400	Weak transcription	A549	lung
43	chr22:31440600-31451000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links