Variant report

Variant	rs2241998
Chromosome Location	chr15:42869028-42869029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42866281..42869584-chr15:42871180..42873707,4	K562	blood:
2	chr15:42840090..42842755-chr15:42865653..42870684,5	K562	blood:
3	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:
4	chr15:42801179..42804150-chr15:42867351..42869271,2	K562	blood:
5	chr15:42867986..42870891-chr15:43024060..43026740,2	K562	blood:

Variant related genes	Relation type
ENSG00000092531	Chromatin interaction
ENSG00000260282	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000261822	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000260490	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10454039	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1060291	0.95[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs10851410	1.00[CEU][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs10851411	1.00[ASW][hapmap];0.86[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11022	1.00[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs11070374	0.95[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11631193	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632169	0.83[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs11636577	0.85[CEU][hapmap]
rs1197546	0.80[ASN][1000 genomes]
rs1197547	0.88[CHB][hapmap];0.84[CHD][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs1211642	0.81[ASN][1000 genomes]
rs12324113	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12324717	1.00[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs12903416	0.80[CHB][hapmap];0.84[AMR][1000 genomes]
rs12903432	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12906697	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1667493	0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1705360	0.83[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs1814518	0.85[ASN][1000 genomes]
rs1900921	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2255995	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2595939	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2595940	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2595941	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2617236	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899051	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2899057	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34643746	0.94[EUR][1000 genomes]
rs3986280	1.00[CEU][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs4447398	0.81[ASN][1000 genomes]
rs4573906	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4923947	0.84[CHD][hapmap]
rs4923948	1.00[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4924684	0.88[EUR][1000 genomes]
rs56357092	0.88[EUR][1000 genomes]
rs60380503	0.87[EUR][1000 genomes]
rs6493053	0.82[AMR][1000 genomes]
rs6493054	0.88[CHB][hapmap];0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs7168835	0.81[CHB][hapmap];0.92[AMR][1000 genomes]
rs8033412	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs876992	0.88[CHB][hapmap];0.87[CHD][hapmap];0.84[ASN][1000 genomes]
rs9302112	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9783683	0.87[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2241998	SNAP23	cis	parietal	SCAN
rs2241998	MAP1A	cis	cerebellum	SCAN
rs2241998	INO80	cis	parietal	SCAN
rs2241998	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs2241998	RINT1	trans	cerebellum	SCAN
rs2241998	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs2241998	MAP1A	cis	parietal	SCAN
rs2241998	TMCO5A	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42867400-42869200	Active TSS	Fetal Muscle Trunk	muscle
2	chr15:42867400-42870200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr15:42867800-42869200	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr15:42868000-42869200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:42868000-42870000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr15:42868200-42869200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
7	chr15:42868200-42869400	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr15:42868200-42869400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr15:42868200-42870400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:42868400-42869200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:42868400-42869200	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr15:42868400-42869200	Active TSS	Colonic Mucosa	Colon
13	chr15:42868400-42869200	Flanking Active TSS	Fetal Heart	heart
14	chr15:42868400-42869200	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr15:42868400-42869400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:42868400-42869400	Flanking Active TSS	GM12878-XiMat	blood
17	chr15:42868400-42873200	Weak transcription	Pancreas	Pancrea
18	chr15:42868600-42869200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr15:42868600-42869200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:42868600-42869200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:42868600-42869200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:42868600-42869200	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr15:42868600-42869400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:42868600-42869400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr15:42868600-42873400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:42868600-42873400	Weak transcription	Gastric	stomach
27	chr15:42868800-42869200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:42868800-42869200	Enhancers	Fetal Brain Male	brain
29	chr15:42868800-42869200	Enhancers	Hela-S3	cervix
30	chr15:42868800-42869200	Enhancers	HMEC	breast
31	chr15:42868800-42869400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:42868800-42869400	Enhancers	Primary B cells from cord blood	blood
33	chr15:42868800-42869400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr15:42868800-42869600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:42868800-42869600	Enhancers	HUVEC	blood vessel
36	chr15:42868800-42869800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:42868800-42869800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:42868800-42869800	Weak transcription	Aorta	Aorta
39	chr15:42868800-42869800	Weak transcription	Psoas Muscle	Psoas
40	chr15:42868800-42869800	Weak transcription	HSMMtube	muscle
41	chr15:42868800-42870000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:42868800-42870000	Enhancers	Brain Anterior Caudate	brain
43	chr15:42868800-42870000	Enhancers	NH-A	brain
44	chr15:42868800-42870800	Enhancers	HSMM	muscle
45	chr15:42868800-42873200	Weak transcription	Lung	lung
46	chr15:42868800-42873200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:42868800-42873200	Weak transcription	Right Ventricle	heart
48	chr15:42868800-42873400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:42868800-42873400	Weak transcription	Spleen	Spleen
50	chr15:42869000-42869200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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