Variant report

Variant	rs34979870
Chromosome Location	chr19:39103764-39103765
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39102966..39104689-chr19:39107783..39109776,2	MCF-7	breast:
2	chr19:39098771..39100599-chr19:39103260..39105890,2	MCF-7	breast:
3	chr19:39103433..39106687-chr19:39106977..39109796,8	K562	blood:
4	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
5	chr19:39101758..39105983-chr19:39106668..39109959,5	K562	blood:

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2232992	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2232997	0.82[ASN][1000 genomes]
rs2277941	0.82[ASN][1000 genomes]
rs34780679	0.90[EUR][1000 genomes];0.80[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34979870	CAPN12	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39087200-39107800	Weak transcription	Colonic Mucosa	Colon
2	chr19:39087400-39107400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr19:39087400-39108200	Weak transcription	Gastric	stomach
4	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
5	chr19:39092600-39109000	Weak transcription	Small Intestine	intestine
6	chr19:39094000-39104600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:39094200-39104200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:39094400-39104200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr19:39094400-39105000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:39094600-39104000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:39094600-39104400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:39094600-39106200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:39094800-39104000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr19:39094800-39106400	Strong transcription	Primary T cells from cord blood	blood
15	chr19:39095400-39104400	Strong transcription	Thymus	Thymus
16	chr19:39095600-39104800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:39095600-39106000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr19:39095800-39106000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:39096200-39104000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:39096200-39105200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:39096800-39108000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:39097800-39108200	Weak transcription	Fetal Intestine Small	intestine
23	chr19:39098400-39104200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:39098600-39108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:39100200-39104200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr19:39100400-39104200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:39101600-39104400	Strong transcription	Primary B cells from cord blood	blood
28	chr19:39102000-39104400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:39102000-39108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:39102200-39107200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:39102200-39107400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39103000-39104000	Strong transcription	Spleen	Spleen
33	chr19:39103000-39105200	Strong transcription	Dnd41	blood
34	chr19:39103200-39106600	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr19:39103200-39107000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:39103400-39106200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:39103600-39104200	Weak transcription	GM12878-XiMat	blood
38	chr19:39103600-39105000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:39103600-39107400	Weak transcription	Fetal Thymus	thymus
40	chr19:39103600-39108000	Weak transcription	Lung	lung
41	chr19:39103600-39108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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