Variant report

Variant	rs5749222
Chromosome Location	chr22:31556759-31556760
allele	C/G
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	CHD1	chr22:31555351-31557255	IMR90	lung:	n/a	n/a
2	CTCF	chr22:31556640-31556790	HUVEC	blood vessel:	n/a	n/a
3	E2F4	chr22:31556707-31556907	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr22:31555839-31556776	ECC-1	luminal epithelium:	n/a	n/a
5	SREBP2	chr22:31555735-31556925	GM12878	blood:	n/a	n/a
6	HCFC1	chr22:31555776-31556788	Hela-S3	cervix:	n/a	n/a
7	UBTF	chr22:31556479-31556766	K562	blood:	n/a	n/a
8	MXI1	chr22:31555745-31557208	SK-N-SH	brain:	n/a	n/a
9	MAX	chr22:31556300-31556792	K562	blood:	n/a	n/a
10	MAZ	chr22:31555772-31556823	IMR90	lung:	n/a	n/a
11	MXI1	chr22:31555846-31557499	IMR90	lung:	n/a	n/a
12	GABPA	chr22:31555381-31556783	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31534966..31537778-chr22:31554685..31557531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214125	TF binding region
MIR3928	TF binding region
ENSG00000100078	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11089493	0.90[JPT][hapmap]
rs17220369	0.85[YRI][hapmap]
rs17820958	0.86[JPT][hapmap]
rs2057951	0.86[JPT][hapmap]
rs2073859	0.91[JPT][hapmap]
rs2073860	0.90[JPT][hapmap]
rs2073861	0.91[JPT][hapmap]
rs2074734	0.86[JPT][hapmap]
rs2240424	0.86[JPT][hapmap]
rs2240427	0.91[JPT][hapmap]
rs2267168	0.90[JPT][hapmap]
rs2283878	0.85[YRI][hapmap]
rs2283882	0.87[JPT][hapmap]
rs2413041	0.85[YRI][hapmap]
rs2899161	0.90[JPT][hapmap]
rs3761430	0.80[JPT][hapmap]
rs4820948	0.93[EUR][1000 genomes]
rs5749224	0.81[AMR][1000 genomes]
rs5749225	0.91[JPT][hapmap]
rs5749232	0.85[YRI][hapmap]
rs5749236	0.91[JPT][hapmap]
rs5749240	0.91[JPT][hapmap]
rs5749252	0.91[JPT][hapmap]
rs5749255	0.90[JPT][hapmap]
rs5753485	0.91[JPT][hapmap]
rs5753486	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5753488	0.85[YRI][hapmap]
rs5753494	0.90[JPT][hapmap]
rs5753495	0.81[JPT][hapmap]
rs5753511	0.90[JPT][hapmap]
rs5753516	0.90[JPT][hapmap]
rs5753519	0.90[JPT][hapmap]
rs5753525	0.90[JPT][hapmap]
rs5753526	0.91[JPT][hapmap]
rs5753527	0.90[JPT][hapmap]
rs5753535	0.90[JPT][hapmap]
rs5753540	0.86[JPT][hapmap]
rs5753551	0.82[YRI][hapmap]
rs5753566	0.90[JPT][hapmap]
rs5753572	0.91[JPT][hapmap]
rs5753574	0.90[JPT][hapmap]
rs5997893	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5997896	0.93[EUR][1000 genomes]
rs5997897	0.93[EUR][1000 genomes]
rs5997921	0.90[JPT][hapmap]
rs5997959	0.86[JPT][hapmap]
rs6518737	0.91[EUR][1000 genomes]
rs713619	0.90[JPT][hapmap]
rs7286926	0.91[JPT][hapmap]
rs7292620	0.91[JPT][hapmap]
rs8135417	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874356	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878718	0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs886074	0.85[YRI][hapmap]
rs9619178	0.91[JPT][hapmap]
rs9621212	0.90[JPT][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	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5749222	DRG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31555000-31556800	Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr22:31555400-31556800	Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr22:31555400-31556800	Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr22:31555400-31556800	Active TSS	Brain Angular Gyrus	brain
5	chr22:31555400-31556800	Active TSS	GM12878-XiMat	blood
6	chr22:31555400-31556800	Active TSS	K562	blood
7	chr22:31555400-31557000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr22:31555400-31557000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:31555400-31557000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr22:31555400-31557000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr22:31555400-31557000	Active TSS	Liver	Liver
12	chr22:31555400-31557000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr22:31555400-31557200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr22:31555400-31557200	Active TSS	NHEK	skin
15	chr22:31555400-31558400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr22:31555600-31556800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:31555600-31556800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr22:31555600-31556800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr22:31555600-31556800	Active TSS	Brain Cingulate Gyrus	brain
20	chr22:31555600-31556800	Active TSS	Brain Hippocampus Middle	brain
21	chr22:31555600-31556800	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr22:31555600-31556800	Active TSS	Brain Substantia Nigra	brain
23	chr22:31555600-31556800	Active TSS	Colon Smooth Muscle	Colon
24	chr22:31555600-31556800	Active TSS	Placenta	Placenta
25	chr22:31555600-31556800	Active TSS	Rectal Smooth Muscle	rectum
26	chr22:31555600-31556800	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr22:31555600-31556800	Active TSS	Hela-S3	cervix
28	chr22:31555600-31556800	Active TSS	NH-A	brain
29	chr22:31555600-31556800	Active TSS	Osteobl	bone
30	chr22:31555600-31557000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr22:31555600-31557000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr22:31555600-31557000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:31555600-31557000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:31555600-31557000	Active TSS	Fetal Kidney	kidney
35	chr22:31555600-31557000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr22:31555600-31557000	Active TSS	Gastric	stomach
37	chr22:31555600-31557000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr22:31555600-31557000	Active TSS	A549	lung
39	chr22:31555600-31557000	Active TSS	HMEC	breast
40	chr22:31555600-31557000	Active TSS	HSMM	muscle
41	chr22:31555600-31557000	Active TSS	NHDF-Ad	bronchial
42	chr22:31555600-31557200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr22:31555600-31557200	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr22:31555600-31557200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr22:31555600-31557200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:31555600-31557200	Active TSS	Colonic Mucosa	Colon
47	chr22:31555600-31557200	Active TSS	Left Ventricle	heart
48	chr22:31555600-31557200	Active TSS	Psoas Muscle	Psoas
49	chr22:31555600-31557200	Active TSS	HSMMtube	muscle
50	chr22:31555600-31557200	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links