Variant report

Variant	rs4779861
Chromosome Location	chr15:31630352-31630353
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	PAX5	chr15:31630339-31631502	GM12878	blood:	n/a	chr15:31630758-31630776 chr15:31630628-31630638 chr15:31631024-31631033 chr15:31631027-31631036
2	MAX	chr15:31630346-31630896	ECC-1	luminal epithelium:	n/a	chr15:31630416-31630425 chr15:31630584-31630593 chr15:31630582-31630592 chr15:31630581-31630596 chr15:31630579-31630594
3	POLR2A	chr15:31629615-31634746	GM12878	blood:	n/a	n/a
4	STAT3	chr15:31630285-31630492	GM12878	blood:	n/a	n/a
5	BHLHE40	chr15:31630351-31630693	GM12878	blood:	n/a	n/a
6	MTA3	chr15:31630211-31631510	GM12878	blood:	n/a	n/a
7	NFIC	chr15:31630340-31631338	ECC-1	luminal epithelium:	n/a	n/a
8	MXI1	chr15:31629939-31631538	GM12878	blood:	n/a	chr15:31630656-31630665 chr15:31631359-31631374 chr15:31631357-31631372 chr15:31630584-31630593
9	TCF12	chr15:31630337-31631324	ECC-1	luminal epithelium:	n/a	n/a
10	WRNIP1	chr15:31630153-31631957	GM12878	blood:	n/a	n/a
11	MAX	chr15:31630178-31631516	NB4	blood:	n/a	chr15:31630416-31630425 chr15:31630584-31630593 chr15:31630582-31630592 chr15:31631359-31631368 chr15:31630581-31630596 chr15:31630579-31630594
12	RELA	chr15:31630329-31631434	GM19099	blood:	n/a	n/a
13	POLR2A	chr15:31630294-31630494	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31623211..31625862-chr15:31627016..31631402,5	K562	blood:

Variant related genes	Relation type
KLF13	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1465778	0.81[GIH][hapmap]
rs2241779	0.91[YRI][hapmap]
rs4779862	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4779863	0.90[YRI][hapmap]
rs4779864	0.84[CHB][hapmap];0.91[YRI][hapmap]
rs56150535	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72722828	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027539	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
13	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
14	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
15	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' 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
16	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
17	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
19	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
20	nsv1052942	chr15:31624164-31653633	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4779861	KLF13	cis	cerebellum	SCAN
rs4779861	SNORD115-40	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31620800-31632600	Enhancers	Fetal Heart	heart
2	chr15:31621600-31637200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:31621800-31630600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:31621800-31636000	Enhancers	Small Intestine	intestine
5	chr15:31621800-31637600	Enhancers	Psoas Muscle	Psoas
6	chr15:31622000-31630600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr15:31622000-31634600	Enhancers	Stomach Mucosa	stomach
8	chr15:31622000-31637600	Enhancers	Left Ventricle	heart
9	chr15:31622200-31630400	Weak transcription	NH-A	brain
10	chr15:31622200-31630600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:31622200-31633200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:31622400-31631600	Enhancers	Right Ventricle	heart
13	chr15:31622600-31630400	Enhancers	Gastric	stomach
14	chr15:31622600-31640200	Enhancers	Pancreas	Pancrea
15	chr15:31622800-31630600	Enhancers	Brain Angular Gyrus	brain
16	chr15:31622800-31657400	Enhancers	Right Atrium	heart
17	chr15:31623000-31630400	Enhancers	Brain Hippocampus Middle	brain
18	chr15:31623000-31630600	Weak transcription	A549	lung
19	chr15:31623400-31637200	Enhancers	Liver	Liver
20	chr15:31623800-31634600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:31624000-31630400	Weak transcription	Fetal Intestine Large	intestine
22	chr15:31624400-31630800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:31624400-31631000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr15:31624400-31631600	Enhancers	Lung	lung
25	chr15:31624400-31634800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:31624400-31635200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr15:31625000-31630400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:31625000-31630400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr15:31625200-31630400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:31625200-31630400	Weak transcription	NHDF-Ad	bronchial
31	chr15:31625200-31649000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:31626000-31638400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:31626200-31630600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:31626200-31633600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr15:31626400-31630600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:31626400-31631800	Enhancers	Esophagus	oesophagus
37	chr15:31626400-31638400	Enhancers	Fetal Muscle Trunk	muscle
38	chr15:31626600-31630400	Genic enhancers	Thymus	Thymus
39	chr15:31626600-31638400	Genic enhancers	Fetal Thymus	thymus
40	chr15:31626800-31630400	Genic enhancers	Primary B cells from cord blood	blood
41	chr15:31627000-31630400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr15:31627000-31630600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:31627000-31630600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr15:31627000-31631200	Genic enhancers	Dnd41	blood
45	chr15:31627000-31632000	Enhancers	Fetal Muscle Leg	muscle
46	chr15:31627000-31637600	Enhancers	Colon Smooth Muscle	Colon
47	chr15:31627200-31631200	Enhancers	Fetal Brain Female	brain
48	chr15:31627200-31635000	Genic enhancers	Primary B cells from peripheral blood	blood
49	chr15:31627200-31635200	Enhancers	Colonic Mucosa	Colon
50	chr15:31627200-31643000	Genic enhancers	Spleen	Spleen

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