Variant report

Variant	rs4347742
Chromosome Location	chr19:39181912-39181913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1031849	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421863	0.86[AMR][1000 genomes]
rs10424568	0.80[ASN][1000 genomes]
rs1060186	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11083476	0.83[AMR][1000 genomes]
rs11665964	0.93[ASN][1000 genomes]
rs11672576	0.86[AMR][1000 genomes]
rs12462503	0.83[ASN][1000 genomes]
rs12984247	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1564203	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985636	0.84[ASN][1000 genomes]
rs2080988	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112649	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112651	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3786841	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786843	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4619518	0.86[AMR][1000 genomes]
rs4801861	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802743	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508813	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508814	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249585	0.86[AMR][1000 genomes]
rs7252630	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749701	0.96[ASN][1000 genomes]
rs752067	0.83[ASN][1000 genomes]
rs755690	0.92[ASN][1000 genomes]
rs8099948	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107877	0.86[AMR][1000 genomes]
rs888996	0.82[ASN][1000 genomes]
rs888997	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936524	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4347742	CAPN12	cis	Muscle Skeletal	GTEx
rs4347742	CAPN12	cis	Adipose Subcutaneous	GTEx
rs4347742	CAPN12	cis	Heart Left Ventricle	GTEx
rs4347742	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs4347742	CAPN12	cis	Esophagus Muscularis	GTEx
rs4347742	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39170000-39183400	Enhancers	Placenta	Placenta
4	chr19:39174800-39182800	Weak transcription	Dnd41	blood
5	chr19:39175600-39182800	Genic enhancers	NHEK	skin
6	chr19:39176400-39182600	Weak transcription	Ovary	ovary
7	chr19:39176800-39182000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:39176800-39182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:39176800-39182800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:39177000-39183000	Weak transcription	Fetal Brain Female	brain
11	chr19:39177200-39182400	Weak transcription	Brain Angular Gyrus	brain
12	chr19:39177200-39182600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:39177400-39182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:39177400-39182400	Weak transcription	Fetal Lung	lung
16	chr19:39177400-39182400	Weak transcription	Gastric	stomach
17	chr19:39177400-39182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:39177400-39182600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr19:39177400-39183400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:39177600-39182400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:39177600-39182600	Weak transcription	Colonic Mucosa	Colon
22	chr19:39177600-39182800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:39177600-39182800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:39177600-39182800	Weak transcription	Primary T cells from cord blood	blood
25	chr19:39177800-39182800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:39178000-39182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:39178000-39182600	Weak transcription	Fetal Thymus	thymus
28	chr19:39178000-39183600	Genic enhancers	Muscle Satellite Cultured Cells	--
29	chr19:39178600-39182400	Weak transcription	Stomach Mucosa	stomach
30	chr19:39178600-39183200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:39178600-39187800	Enhancers	Left Ventricle	heart
32	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
34	chr19:39178800-39182600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:39179400-39182400	Weak transcription	Esophagus	oesophagus
37	chr19:39179400-39184400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr19:39179600-39182600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:39179600-39182600	Weak transcription	GM12878-XiMat	blood
40	chr19:39179600-39183400	Weak transcription	Primary B cells from cord blood	blood
41	chr19:39179600-39183600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr19:39179800-39182400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr19:39179800-39183800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39180000-39182000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:39180000-39182000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:39180000-39182000	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:39180000-39182200	Strong transcription	Fetal Stomach	stomach
49	chr19:39180000-39182400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:39180000-39182400	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links