Variant report

Variant	rs877549
Chromosome Location	chr22:30672420-30672421
allele	A/G
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30660224..30662293-chr22:30672122..30673806,2	K562	blood:
2	chr22:30668087..30672476-chr22:30679635..30681942,4	K562	blood:
3	chr22:30671566..30674215-chr22:30702631..30704760,2	MCF-7	breast:
4	chr22:30671223..30673243-chr22:30676654..30678406,2	MCF-7	breast:
5	chr22:30669173..30672631-chr22:30679828..30683930,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GATSL3-2	chr22:30671204-30672940	NONHSAT084762

No data

Variant related genes	Relation type
ENSG00000099985	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000239282	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1076296	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap]
rs11913990	0.87[LWK][hapmap]
rs4320024	0.91[AMR][1000 genomes]
rs5753118	0.82[ASW][hapmap];0.90[CEU][hapmap]
rs5763928	0.84[LWK][hapmap];0.81[AFR][1000 genomes]
rs57908818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58874195	0.87[AFR][1000 genomes]
rs60111450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737948	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv588885	chr22:30661184-30691631	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs877549	NIPSNAP1	cis	cerebellum	SCAN
rs877549	TPST2	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30659600-30673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr22:30662800-30673400	Weak transcription	Right Atrium	heart
3	chr22:30663600-30673800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:30663800-30674000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:30664000-30673000	Weak transcription	Colonic Mucosa	Colon
6	chr22:30668000-30673600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr22:30669400-30676800	Enhancers	Adipose Nuclei	Adipose
8	chr22:30670000-30673200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr22:30670200-30673000	Weak transcription	Osteobl	bone
10	chr22:30670200-30673400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:30670200-30673600	Weak transcription	Brain Substantia Nigra	brain
12	chr22:30670200-30673800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:30670400-30673000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr22:30670400-30673000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:30670400-30673800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr22:30670400-30673800	Weak transcription	Brain Hippocampus Middle	brain
17	chr22:30670400-30673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr22:30670400-30674400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr22:30670600-30674000	Weak transcription	Brain Anterior Caudate	brain
20	chr22:30671000-30672600	Flanking Active TSS	Dnd41	blood
21	chr22:30671000-30673800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr22:30671000-30674200	Weak transcription	Lung	lung
23	chr22:30671200-30672600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:30671200-30672600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr22:30671200-30672800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
26	chr22:30671400-30672600	Enhancers	Fetal Thymus	thymus
27	chr22:30671400-30672600	Enhancers	Thymus	Thymus
28	chr22:30671400-30672800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr22:30671400-30674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr22:30671600-30672600	Enhancers	Primary T cells from cord blood	blood
31	chr22:30671600-30672600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr22:30671600-30673200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr22:30671600-30674000	Enhancers	Duodenum Mucosa	Duodenum
34	chr22:30671600-30674600	Enhancers	Primary hematopoietic stem cells	blood
35	chr22:30671600-30675600	Enhancers	Fetal Intestine Small	intestine
36	chr22:30671800-30672600	Enhancers	Primary B cells from peripheral blood	blood
37	chr22:30671800-30674400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr22:30672000-30673000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:30672000-30673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr22:30672000-30674000	Weak transcription	Esophagus	oesophagus
41	chr22:30672200-30672600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:30672200-30672600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr22:30672200-30672600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr22:30672200-30672600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr22:30672200-30672800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr22:30672200-30672800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr22:30672200-30672800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr22:30672200-30672800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr22:30672200-30673000	Weak transcription	NHEK	skin
50	chr22:30672200-30673200	Weak transcription	Fetal Intestine Large	intestine

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