Variant report

Variant	rs4977738
Chromosome Location	chr9:21875506-21875507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64371132..64371903-chr9:21875222..21876218,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000197329	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10117550	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118406	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10965174	0.83[CEU][hapmap]
rs1134871	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11526324	0.83[CEU][hapmap]
rs11531716	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12553901	0.83[CEU][hapmap]
rs1418072	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2027484	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3928893	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4352938	0.83[CEU][hapmap]
rs4593639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4607704	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4607709	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977569	0.83[CEU][hapmap]
rs4977737	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4977739	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6475592	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028211	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7047648	0.87[GIH][hapmap]
rs756641	0.83[CEU][hapmap]
rs7865071	0.83[CEU][hapmap]

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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4977738	MTAP	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21855600-21879800	Weak transcription	Small Intestine	intestine
2	chr9:21857400-21883800	Weak transcription	Pancreas	Pancrea
3	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:21860200-21879800	Weak transcription	Right Ventricle	heart
5	chr9:21862200-21886800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:21863200-21880800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:21864800-21879400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:21865000-21880800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:21865000-21890200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:21865400-21892600	Weak transcription	Colonic Mucosa	Colon
11	chr9:21865600-21879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:21865600-21890000	Weak transcription	Placenta	Placenta
13	chr9:21865800-21876600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:21865800-21879400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:21865800-21879400	Weak transcription	Liver	Liver
16	chr9:21865800-21879400	Weak transcription	GM12878-XiMat	blood
17	chr9:21865800-21879600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr9:21865800-21879800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:21865800-21880200	Weak transcription	Gastric	stomach
20	chr9:21865800-21882200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr9:21865800-21883200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:21865800-21886800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:21865800-21889600	Weak transcription	Ovary	ovary
24	chr9:21866000-21875600	Weak transcription	Fetal Lung	lung
25	chr9:21866000-21883800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:21866000-21886000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:21866000-21890200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:21866800-21883400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:21869000-21875600	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:21869000-21881600	Weak transcription	Lung	lung
31	chr9:21869000-21883600	Weak transcription	Aorta	Aorta
32	chr9:21869400-21880200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:21869400-21889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:21869600-21880600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:21869600-21890000	Weak transcription	Thymus	Thymus
36	chr9:21869800-21875600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:21869800-21879400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr9:21869800-21880200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:21870000-21877200	Weak transcription	Primary T cells from cord blood	blood
40	chr9:21870000-21880200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:21870200-21875600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr9:21870200-21875600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:21870200-21879800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:21870200-21880200	Weak transcription	Adipose Nuclei	Adipose
45	chr9:21870200-21880200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr9:21870200-21889600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:21871800-21876800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:21872200-21879400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:21873000-21881800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr9:21873000-21893000	Weak transcription	NHDF-Ad	bronchial

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