Variant report

Variant	rs11630449
Chromosome Location	chr15:31614741-31614742
allele	C/T
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	RAD21	chr15:31614624-31615022	HepG2	liver:	n/a	n/a
2	SMC3	chr15:31614694-31614963	HepG2	liver:	n/a	n/a
3	RAD21	chr15:31614655-31615014	HepG2	liver:	n/a	n/a
4	RAD21	chr15:31614706-31614979	HepG2	liver:	n/a	n/a
5	POLR2A	chr15:31614375-31615142	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:31614685-31614968	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:31612703..31615766-chr15:31616298..31621086,4	K562	blood:
2	chr15:31600316..31602672-chr15:31614441..31616388,2	K562	blood:
3	chr15:31613330..31614958-chr15:31617530..31619588,2	MCF-7	breast:

Variant related genes	Relation type
KLF13	TF binding region
ENSG00000169926	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11070920	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070922	0.83[AFR][1000 genomes]
rs11070943	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439534	0.85[AFR][1000 genomes]
rs12595077	0.83[AFR][1000 genomes]
rs12899315	0.83[AFR][1000 genomes]
rs12913847	0.81[EUR][1000 genomes]
rs2338700	1.00[YRI][hapmap]
rs2879243	0.83[AFR][1000 genomes]
rs34784107	0.87[AFR][1000 genomes]
rs6493604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039367	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv542318	chr15:31601016-31628938	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv542319	chr15:31605961-31628938	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11630449	SNORD115-48	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31606800-31617200	Weak transcription	Spleen	Spleen
2	chr15:31607800-31615800	Enhancers	Thymus	Thymus
3	chr15:31607800-31616800	Enhancers	Fetal Thymus	thymus
4	chr15:31609200-31617000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:31609600-31616800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:31609800-31616000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:31610000-31616600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:31610000-31616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:31610400-31616200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:31610400-31617000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:31610400-31617200	Weak transcription	Fetal Brain Female	brain
12	chr15:31610600-31616000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:31610800-31616200	Weak transcription	Fetal Lung	lung
14	chr15:31610800-31617000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:31612000-31617000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:31612200-31615000	Weak transcription	Primary B cells from cord blood	blood
17	chr15:31612400-31617000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:31612600-31614800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:31612800-31616800	Weak transcription	Dnd41	blood
20	chr15:31613000-31615200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:31613200-31614800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr15:31613800-31616400	Weak transcription	Stomach Mucosa	stomach
23	chr15:31613800-31617000	Weak transcription	Esophagus	oesophagus
24	chr15:31614000-31615000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:31614000-31616400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:31614200-31614800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:31614200-31614800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr15:31614400-31614800	Enhancers	Fetal Intestine Large	intestine
29	chr15:31614400-31615600	Enhancers	HepG2	liver
30	chr15:31614600-31615000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:31614600-31615200	Enhancers	Fetal Intestine Small	intestine
32	chr15:31614600-31616200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:31614600-31617000	Enhancers	Primary T cells from cord blood	blood

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