Variant report

Variant	rs2459634
Chromosome Location	chr19:39041477-39041478
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39039848..39042525-chr19:39107323..39110134,2	MCF-7	breast:
2	chr19:39041206..39043437-chr19:39108785..39111389,2	K562	blood:
3	chr19:39041080..39043416-chr19:39085645..39088550,3	K562	blood:
4	chr19:39038810..39041650-chr19:39063092..39065838,2	K562	blood:
5	chr19:39033355..39037027-chr19:39040774..39043679,3	K562	blood:
6	chr19:39040122..39042064-chr19:39047270..39049088,2	K562	blood:

Variant related genes	Relation type
ENSG00000267291	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2071089	0.80[EUR][1000 genomes]
rs2960347	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv1058902	chr19:39025940-39078574	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1064490	chr19:39029788-39078574	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2459634	CAPN12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
2	chr19:39026000-39052400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39029000-39051600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:39029600-39046000	Weak transcription	HSMM	muscle
5	chr19:39030000-39054600	Strong transcription	Fetal Muscle Leg	muscle
6	chr19:39030200-39055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr19:39034600-39051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:39035200-39042400	Weak transcription	Spleen	Spleen
9	chr19:39035200-39052600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39035200-39066400	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr19:39035600-39050800	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:39035600-39051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:39035600-39052000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:39035600-39052000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:39035600-39052000	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:39035800-39041800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:39035800-39044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:39035800-39044600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:39035800-39045000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:39035800-39047400	Weak transcription	A549	lung
21	chr19:39035800-39051800	Weak transcription	Brain Anterior Caudate	brain
22	chr19:39036000-39051800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:39036000-39076400	Weak transcription	Brain Substantia Nigra	brain
24	chr19:39037000-39043800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr19:39037200-39051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:39038400-39047200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr19:39039000-39042000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:39039200-39051800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:39039800-39052200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:39040000-39042000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:39040000-39050000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:39040000-39054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:39040800-39041600	Enhancers	Brain Germinal Matrix	brain
34	chr19:39040800-39042600	Enhancers	K562	blood
35	chr19:39041000-39042200	Weak transcription	HSMMtube	muscle
36	chr19:39041400-39042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:39041400-39042400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr19:39041400-39042600	Enhancers	GM12878-XiMat	blood
39	chr19:39041400-39050800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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