Variant report

Variant	rs3810341
Chromosome Location	chr19:39156481-39156482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39136593..39141523-chr19:39155434..39158627,5	K562	blood:
2	chr19:39153844..39156504-chr19:39338574..39341017,2	K562	blood:
3	chr19:39156222..39158028-chr19:39160453..39162596,3	K562	blood:
4	chr19:39155095..39156706-chr19:39341962..39343688,2	MCF-7	breast:
5	chr19:39154055..39157137-chr19:39203619..39206563,4	MCF-7	breast:
6	chr19:39156254..39158028-chr19:39160745..39162596,2	K562	blood:
7	chr19:39156320..39158010-chr19:39194511..39197034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10403540	0.86[ASN][1000 genomes]
rs10404257	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10406778	0.87[ASN][1000 genomes]
rs10415219	0.98[ASN][1000 genomes]
rs10415646	0.83[ASN][1000 genomes]
rs10421560	0.81[ASN][1000 genomes]
rs11083475	0.81[ASN][1000 genomes]
rs12460849	0.95[ASN][1000 genomes]
rs12462270	0.83[ASN][1000 genomes]
rs13343794	0.83[ASN][1000 genomes]
rs16972767	0.99[ASN][1000 genomes]
rs2279144	0.83[ASN][1000 genomes]
rs28488032	0.85[ASN][1000 genomes]
rs28624276	0.85[ASN][1000 genomes]
rs3745859	0.83[ASN][1000 genomes]
rs3786835	0.99[ASN][1000 genomes]
rs3786845	0.83[ASN][1000 genomes]
rs3786848	0.85[ASN][1000 genomes]
rs3786851	0.83[ASN][1000 genomes]
rs55876653	0.98[ASN][1000 genomes]
rs56113315	0.80[ASN][1000 genomes]
rs56365761	0.98[ASN][1000 genomes]
rs62121814	0.97[ASN][1000 genomes]
rs62121816	0.89[ASN][1000 genomes]
rs62121818	0.87[ASN][1000 genomes]
rs7252589	0.87[ASN][1000 genomes]
rs7254100	0.85[ASN][1000 genomes]
rs8111746	0.83[ASN][1000 genomes]
rs883433	0.85[ASN][1000 genomes]
rs979971	0.98[ASN][1000 genomes]
rs979972	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv960837	chr19:39156364-39162333	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3810341	CAPN12	cis	Esophagus Muscularis	GTEx
rs3810341	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs3810341	CAPN12	cis	Adipose Subcutaneous	GTEx
rs3810341	CAPN12	cis	Heart Left Ventricle	GTEx
rs3810341	CTD-2540F13.2	cis	Esophagus Muscularis	GTEx
rs3810341	CAPN12	cis	Muscle Skeletal	GTEx
rs3810341	CTD-2540F13.2	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39147800-39160800	Enhancers	Placenta	Placenta
4	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
5	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
6	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
8	chr19:39151400-39157400	Genic enhancers	NHLF	lung
9	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr19:39151800-39156800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39152000-39159800	Weak transcription	Dnd41	blood
12	chr19:39152400-39159200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:39152400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:39152600-39156600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr19:39152600-39157600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:39152600-39157600	Enhancers	Fetal Lung	lung
17	chr19:39152600-39158400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:39152600-39158600	Enhancers	Ovary	ovary
19	chr19:39152600-39159200	Enhancers	Colonic Mucosa	Colon
20	chr19:39152600-39160000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:39152600-39160000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr19:39152600-39162200	Enhancers	Spleen	Spleen
23	chr19:39152600-39164000	Enhancers	Liver	Liver
24	chr19:39152800-39157000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr19:39152800-39157600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:39152800-39157600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr19:39152800-39159400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:39152800-39161200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39153000-39157000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:39153000-39157200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:39153000-39157200	Enhancers	HUVEC	blood vessel
32	chr19:39153000-39158000	Enhancers	Gastric	stomach
33	chr19:39153000-39158400	Enhancers	Primary B cells from cord blood	blood
34	chr19:39153000-39158600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:39153000-39161200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr19:39153200-39157400	Enhancers	NH-A	brain
37	chr19:39153200-39159200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:39153400-39157200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:39153400-39157400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr19:39153400-39159400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39153400-39161200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:39154000-39158800	Transcr. at gene 5' and 3'	A549	lung
43	chr19:39154000-39160200	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:39154000-39160400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
45	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
46	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
47	chr19:39154200-39156600	Flanking Active TSS	Fetal Heart	heart
48	chr19:39154200-39158000	Bivalent Enhancer	Fetal Thymus	thymus
49	chr19:39154200-39158600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr19:39154200-39160000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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