Variant report

Variant	rs12429554
Chromosome Location	chr13:49613208-49613209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49612653..49615001-chr13:49616623..49619316,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1159972	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11617719	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11620305	0.91[EUR][1000 genomes]
rs17477129	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs35468616	0.83[AMR][1000 genomes]
rs61950726	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61950727	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61950730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7990472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12429554	KCNRG	cis	cerebellum	SCAN
rs12429554	CAB39L	cis	cerebellum	SCAN
rs12429554	SNORA31	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49557000-49626800	Weak transcription	Right Ventricle	heart
3	chr13:49568800-49626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:49568800-49627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:49573400-49634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:49582800-49617600	Weak transcription	Liver	Liver
8	chr13:49584000-49616600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:49584200-49649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:49584600-49613800	Weak transcription	Left Ventricle	heart
11	chr13:49587800-49626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:49592800-49649600	Weak transcription	Fetal Intestine Large	intestine
13	chr13:49594800-49636000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr13:49596400-49626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:49597200-49619600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr13:49597200-49626600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:49598000-49650200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr13:49598600-49626800	Weak transcription	Osteobl	bone
19	chr13:49598800-49617600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:49599000-49614200	Weak transcription	Hela-S3	cervix
21	chr13:49599000-49649200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr13:49601000-49616200	Weak transcription	Fetal Lung	lung
23	chr13:49601400-49620400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:49601600-49620000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:49601600-49623800	Weak transcription	Fetal Stomach	stomach
26	chr13:49601800-49660600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:49603200-49649200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr13:49603200-49652200	Weak transcription	Dnd41	blood
29	chr13:49603400-49613400	Weak transcription	Placenta	Placenta
30	chr13:49603400-49623800	Weak transcription	Fetal Intestine Small	intestine
31	chr13:49604600-49625200	Weak transcription	Primary B cells from cord blood	blood
32	chr13:49604600-49626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:49604800-49618800	Weak transcription	GM12878-XiMat	blood
34	chr13:49604800-49636400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:49605200-49643400	Weak transcription	HSMM	muscle
36	chr13:49605600-49613800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:49607800-49627000	Weak transcription	HMEC	breast
38	chr13:49608800-49638800	Weak transcription	Ovary	ovary
39	chr13:49608800-49658800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr13:49610000-49619400	Weak transcription	Gastric	stomach
41	chr13:49610800-49620200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr13:49611000-49620600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:49611600-49620800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr13:49611600-49625000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:49612000-49614800	Weak transcription	Esophagus	oesophagus
46	chr13:49612200-49616400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr13:49612400-49618200	Weak transcription	Primary T cells from cord blood	blood
48	chr13:49612600-49618000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:49612600-49626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr13:49612600-49628600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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