Variant report

Variant	rs132549
Chromosome Location	chr22:29318724-29318725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10854810	1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs5762763	1.00[LWK][hapmap]
rs5762783	0.93[AFR][1000 genomes]
rs9608698	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs132549	RNF215	cis	parietal	SCAN
rs132549	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29314200-29319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:29314400-29318800	Weak transcription	HMEC	breast
3	chr22:29314400-29342800	Weak transcription	Brain Substantia Nigra	brain
4	chr22:29314600-29321800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr22:29314800-29319800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:29314800-29319800	Weak transcription	NH-A	brain
7	chr22:29314800-29328400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr22:29315000-29319800	Weak transcription	Psoas Muscle	Psoas
9	chr22:29315200-29318800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:29315200-29318800	Weak transcription	Gastric	stomach
11	chr22:29315200-29319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:29315200-29319200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr22:29315200-29319800	Weak transcription	Fetal Brain Male	brain
14	chr22:29315200-29319800	Weak transcription	Left Ventricle	heart
15	chr22:29315200-29326400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29315400-29319000	Weak transcription	Brain Angular Gyrus	brain
17	chr22:29315400-29319800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr22:29315800-29325000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr22:29316400-29322600	Enhancers	Fetal Lung	lung
20	chr22:29316600-29319600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr22:29316600-29320000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:29316600-29322600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:29316800-29319800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr22:29317000-29321000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:29317200-29319600	Weak transcription	Fetal Muscle Leg	muscle
26	chr22:29317200-29319600	Enhancers	Stomach Smooth Muscle	stomach
27	chr22:29317200-29319800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr22:29317200-29322000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:29317400-29318800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr22:29317400-29319600	Weak transcription	Brain Germinal Matrix	brain
31	chr22:29317400-29319800	Enhancers	NHEK	skin
32	chr22:29317600-29319000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:29317600-29319000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr22:29317600-29319200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr22:29317600-29319200	Weak transcription	A549	lung
36	chr22:29317600-29319800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr22:29317600-29319800	Weak transcription	Brain Anterior Caudate	brain
38	chr22:29317600-29319800	Weak transcription	Fetal Brain Female	brain
39	chr22:29317600-29321800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:29317600-29325400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr22:29317800-29318800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:29317800-29319000	Weak transcription	Colon Smooth Muscle	Colon
43	chr22:29317800-29319800	Weak transcription	Esophagus	oesophagus
44	chr22:29317800-29321200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr22:29317800-29321400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr22:29317800-29329400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:29318000-29320200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr22:29318200-29318800	Flanking Active TSS	HepG2	liver
49	chr22:29318200-29319600	Enhancers	Liver	Liver
50	chr22:29318200-29326600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links