Variant report

Variant	rs12989898
Chromosome Location	chr2:55824793-55824794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55816894..55821327-chr2:55821705..55825491,6	K562	blood:
2	chr2:55823780..55826552-chr2:55827619..55830389,2	K562	blood:
3	chr2:55824426..55829337-chr2:55843280..55847413,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10184287	0.80[JPT][hapmap]
rs10195281	0.82[AFR][1000 genomes]
rs10200159	0.82[AFR][1000 genomes]
rs10203953	0.84[AFR][1000 genomes]
rs10221888	0.81[YRI][hapmap]
rs1037508	0.90[ASN][1000 genomes]
rs10427222	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1045910	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10496044	0.83[YRI][hapmap]
rs10496049	0.87[YRI][hapmap]
rs11890141	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11900763	1.00[CEU][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12463766	0.90[ASN][1000 genomes]
rs12616502	0.97[YRI][hapmap]
rs12619756	0.85[ASN][1000 genomes]
rs13016772	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028892	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs13382187	0.84[YRI][hapmap]
rs13383352	0.84[YRI][hapmap]
rs13403782	0.85[ASN][1000 genomes]
rs13407344	0.84[YRI][hapmap]
rs1373228	0.83[JPT][hapmap]
rs1563201	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17047094	0.97[YRI][hapmap];0.84[AFR][1000 genomes]
rs17047119	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs1814457	0.81[ASN][1000 genomes]
rs1975486	0.91[JPT][hapmap]
rs2168097	0.82[ASN][1000 genomes]
rs2586946	0.87[ASN][1000 genomes]
rs2586948	0.87[ASN][1000 genomes]
rs2586949	0.87[JPT][hapmap]
rs2586965	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2627758	0.88[ASN][1000 genomes]
rs2627763	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2627778	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2627783	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748945	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3748955	0.86[AFR][1000 genomes]
rs3816489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233962	0.90[ASN][1000 genomes]
rs4671248	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs4671250	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165178	0.91[ASN][1000 genomes]
rs6545503	0.90[JPT][hapmap]
rs6545505	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6545507	0.82[AFR][1000 genomes]
rs6545508	0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs6545510	0.97[YRI][hapmap];0.83[AFR][1000 genomes]
rs6545513	0.83[YRI][hapmap]
rs6712314	0.82[AFR][1000 genomes]
rs6716100	0.83[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs6717574	0.96[YRI][hapmap]
rs6731927	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6736996	0.90[AFR][1000 genomes]
rs6739788	0.89[YRI][hapmap]
rs6745430	0.95[AFR][1000 genomes]
rs6745650	0.96[YRI][hapmap]
rs6760959	0.97[YRI][hapmap];0.89[AFR][1000 genomes]
rs730884	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736345	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs744514	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7558127	0.81[YRI][hapmap]
rs7571482	0.87[ASN][1000 genomes]
rs7574398	0.89[AFR][1000 genomes]
rs7574409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7585484	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7594497	0.83[YRI][hapmap]
rs7605486	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7605504	0.84[ASN][1000 genomes]
rs782574	0.83[JPT][hapmap]
rs782589	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs782591	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs782593	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs782597	0.81[ASN][1000 genomes]
rs782598	0.87[ASN][1000 genomes]
rs782603	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs782612	0.88[ASN][1000 genomes]
rs782648	0.84[ASN][1000 genomes]
rs782651	0.84[ASN][1000 genomes]
rs9309267	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs9309268	0.81[AFR][1000 genomes]
rs9636439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12989898	SMEK2	Cis_1M	lymphoblastoid	RTeQTL
rs12989898	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
7	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
8	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
12	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
13	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
15	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:55797000-55829600	Weak transcription	Gastric	stomach
17	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:55804400-55825200	Weak transcription	K562	blood
19	chr2:55806600-55825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:55806800-55825200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:55808200-55824800	Weak transcription	Colonic Mucosa	Colon
22	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
23	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:55811600-55825000	Weak transcription	Fetal Brain Female	brain
25	chr2:55814200-55825200	Weak transcription	HUVEC	blood vessel
26	chr2:55814200-55825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain
29	chr2:55814400-55826000	Weak transcription	GM12878-XiMat	blood
30	chr2:55815200-55825400	Weak transcription	Hela-S3	cervix
31	chr2:55816000-55824800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:55816200-55825000	Weak transcription	Placenta	Placenta
33	chr2:55816400-55825200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:55818000-55827400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:55818400-55825000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:55818400-55825000	Weak transcription	A549	lung
37	chr2:55818400-55825000	Weak transcription	Osteobl	bone
38	chr2:55818400-55825400	Weak transcription	NH-A	brain
39	chr2:55818400-55825600	Weak transcription	NHDF-Ad	bronchial
40	chr2:55818400-55825800	Weak transcription	NHLF	lung
41	chr2:55818600-55825400	Weak transcription	HMEC	breast
42	chr2:55818600-55834400	Weak transcription	Small Intestine	intestine
43	chr2:55818600-55835200	Weak transcription	Psoas Muscle	Psoas
44	chr2:55819000-55825400	Weak transcription	NHEK	skin
45	chr2:55820200-55831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:55820400-55826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:55820400-55830400	Strong transcription	Fetal Intestine Large	intestine
48	chr2:55820600-55826400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:55820600-55830600	Strong transcription	Dnd41	blood
50	chr2:55820600-55832000	Strong transcription	Primary B cells from peripheral blood	blood

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