Variant report

Variant	rs8042404
Chromosome Location	chr15:31680016-31680017
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	chr15:31673644..31676164-chr15:31678034..31680929,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10459614	0.86[ASN][1000 genomes]
rs10851544	0.87[ASN][1000 genomes]
rs10851545	0.87[ASN][1000 genomes]
rs11630067	0.82[ASN][1000 genomes]
rs11630485	0.82[ASN][1000 genomes]
rs11631345	0.87[ASN][1000 genomes]
rs11636300	0.86[ASN][1000 genomes]
rs11638964	0.80[ASN][1000 genomes]
rs11639133	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12441543	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12441765	0.82[ASN][1000 genomes]
rs12594811	0.82[ASN][1000 genomes]
rs12902234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910502	0.82[ASN][1000 genomes]
rs12912800	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34482222	0.86[ASN][1000 genomes]
rs4346167	0.80[ASN][1000 genomes]
rs4558376	0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4606678	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs4613031	0.87[ASN][1000 genomes]
rs4779523	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4779525	0.86[ASN][1000 genomes]
rs4779526	0.82[ASN][1000 genomes]
rs59970767	0.95[ASN][1000 genomes]
rs6493652	0.82[ASN][1000 genomes]
rs7165900	0.81[ASN][1000 genomes]
rs7170922	0.80[ASN][1000 genomes]
rs7171667	0.87[ASN][1000 genomes]
rs7174902	0.81[ASN][1000 genomes]
rs7402977	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs7496920	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs8030771	0.84[ASN][1000 genomes]
rs8035633	0.82[ASN][1000 genomes]
rs8043195	0.89[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	esv1810782	chr15:31633161-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
13	nsv903843	chr15:31672947-31723279	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8042404	KLF13	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31670800-31683800	Weak transcription	Small Intestine	intestine
2	chr15:31673600-31684000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:31674200-31684000	Weak transcription	Colonic Mucosa	Colon
4	chr15:31674600-31683800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:31674600-31684000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:31675000-31684000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:31675200-31681600	Weak transcription	Fetal Stomach	stomach
8	chr15:31675200-31684000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:31675800-31683800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:31675800-31683800	Weak transcription	Right Atrium	heart
11	chr15:31675800-31684000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:31676600-31683000	Weak transcription	Fetal Intestine Large	intestine
13	chr15:31676800-31681000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:31676800-31681000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr15:31677000-31681000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr15:31677000-31683400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr15:31677000-31684000	Weak transcription	Gastric	stomach
18	chr15:31677200-31680800	Enhancers	Primary T cells from cord blood	blood
19	chr15:31677200-31681200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:31677200-31681600	Weak transcription	Primary B cells from cord blood	blood
21	chr15:31677400-31681800	Weak transcription	Left Ventricle	heart
22	chr15:31677600-31680200	Enhancers	Right Ventricle	heart
23	chr15:31677600-31681200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr15:31677800-31680400	Enhancers	Fetal Thymus	thymus
25	chr15:31677800-31680400	Enhancers	Thymus	Thymus
26	chr15:31677800-31680600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr15:31677800-31680600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:31678600-31680800	Enhancers	Dnd41	blood
29	chr15:31678800-31680400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:31678800-31680800	Enhancers	Fetal Heart	heart
31	chr15:31679200-31680200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:31679200-31680400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:31679200-31680600	Enhancers	Liver	Liver
34	chr15:31679200-31681400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:31679400-31680400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:31679400-31680400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:31679400-31680400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:31679400-31680600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:31679400-31680600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:31679400-31680600	Enhancers	Fetal Brain Female	brain
41	chr15:31679400-31680600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:31679400-31680600	Enhancers	HSMM	muscle
43	chr15:31679400-31680600	Enhancers	NH-A	brain
44	chr15:31679400-31680600	Enhancers	NHEK	skin
45	chr15:31679400-31680800	Enhancers	Pancreas	Pancrea
46	chr15:31679400-31680800	Enhancers	Stomach Mucosa	stomach
47	chr15:31679400-31680800	Enhancers	HMEC	breast
48	chr15:31679400-31681400	Enhancers	NHDF-Ad	bronchial
49	chr15:31679400-31682200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr15:31679800-31680200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links