Variant report

Variant	rs34780679
Chromosome Location	chr19:39110649-39110650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr19:39108662-39110703	A549	lung:	n/a	chr19:39110689-39110696
2	ELK1	chr19:39110571-39110663	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39110338-39110915	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:39108616-39111427	K562	blood:	n/a	n/a
5	EP300	chr19:39108886-39110695	A549	lung:	n/a	n/a
6	POLR2A	chr19:39108805-39110710	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39110591-39110687	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:39107795-39111328	GM12878	blood:	n/a	n/a
9	SIN3AK20	chr19:39108443-39111312	PANC-1	pancreas:	n/a	n/a
10	BCL3	chr19:39108731-39110848	A549	lung:	n/a	chr19:39109262-39109275 chr19:39110004-39110013 chr19:39109603-39109616 chr19:39110055-39110068 chr19:39108867-39108876
11	GABPA	chr19:39108902-39110657	A549	lung:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109023-39109034 chr19:39109023-39109032 chr19:39109624-39109638 chr19:39109020-39109034 chr19:39109687-39109701 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
12	POLR2A	chr19:39110382-39110862	K562	blood:	n/a	n/a
13	MAX	chr19:39110287-39110811	K562	blood:	n/a	n/a
14	POLR2A	chr19:39108158-39113791	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:39108539-39110828	K562	blood:	n/a	n/a
16	SIN3AK20	chr19:39108740-39110899	PANC-1	pancreas:	n/a	n/a
17	GABPA	chr19:39109170-39110750	MCF-7	breast:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109624-39109638 chr19:39109687-39109701 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
18	POLR2A	chr19:39110510-39110781	GM12878	blood:	n/a	n/a
19	WRNIP1	chr19:39108046-39110666	GM12878	blood:	n/a	n/a
20	GABPA	chr19:39108876-39110812	A549	lung:	n/a	chr19:39109690-39109701 chr19:39109626-39109635 chr19:39109023-39109034 chr19:39109023-39109032 chr19:39109624-39109638 chr19:39109020-39109034 chr19:39109687-39109701 chr19:39109690-39109699 chr19:39109624-39109635 chr19:39109603-39109612
21	MXI1	chr19:39108662-39110844	SK-N-SH	brain:	n/a	chr19:39109722-39109731
22	MAX	chr19:39108636-39111143	A549	lung:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39108656-39108666 chr19:39109718-39109737 chr19:39108653-39108663 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734
23	SP1	chr19:39108780-39110782	A549	lung:	n/a	chr19:39108867-39108876 chr19:39108867-39108877 chr19:39109601-39109613 chr19:39109603-39109612 chr19:39108866-39108878 chr19:39109602-39109612 chr19:39108868-39108877 chr19:39109602-39109616 chr19:39109602-39109611 chr19:39109602-39109611 chr19:39108868-39108881 chr19:39109602-39109612 chr19:39108866-39108878 chr19:39109601-39109613
24	POLR2A	chr19:39108454-39110922	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr19:39110506-39110785	GM12878	blood:	n/a	n/a
26	MXI1	chr19:39108779-39110800	IMR90	lung:	n/a	chr19:39109722-39109731
27	POLR2A	chr19:39108715-39110655	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
2	chr19:39109034..39110948-chr19:39138125..39139962,2	MCF-7	breast:
3	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
4	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
5	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
6	chr19:39109264..39111637-chr19:39122200..39124366,4	MCF-7	breast:
7	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
8	chr19:39108186..39111004-chr19:39340137..39342268,2	K562	blood:
9	chr19:39110019..39112563-chr19:39114565..39116465,2	MCF-7	breast:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000178982	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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2232997	0.90[ASN][1000 genomes]
rs2277941	0.90[ASN][1000 genomes]
rs34979870	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
rs34780679	CAPN12	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39107800-39111000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:39108400-39111000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr19:39109000-39110800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:39109200-39110800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:39109200-39110800	Active TSS	A549	lung
6	chr19:39109200-39111000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:39109400-39110800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:39109800-39111000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr19:39109800-39111200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
10	chr19:39110000-39110800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr19:39110000-39110800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr19:39110000-39110800	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr19:39110000-39110800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr19:39110000-39110800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr19:39110000-39110800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39110000-39110800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:39110000-39111000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr19:39110200-39110800	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr19:39110200-39110800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr19:39110200-39110800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr19:39110200-39110800	Flanking Active TSS	Liver	Liver
22	chr19:39110200-39110800	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr19:39110200-39110800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr19:39110200-39110800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr19:39110200-39110800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr19:39110200-39110800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr19:39110200-39110800	Flanking Active TSS	Fetal Brain Male	brain
28	chr19:39110200-39110800	Flanking Active TSS	Fetal Brain Female	brain
29	chr19:39110200-39110800	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr19:39110200-39110800	Flanking Active TSS	Fetal Stomach	stomach
31	chr19:39110200-39110800	Flanking Active TSS	Fetal Thymus	thymus
32	chr19:39110200-39110800	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr19:39110200-39110800	Flanking Active TSS	HSMMtube	muscle
34	chr19:39110200-39110800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr19:39110200-39111000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:39110200-39111000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr19:39110200-39111000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr19:39110200-39111000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:39110200-39111000	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr19:39110200-39111000	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr19:39110200-39111000	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr19:39110200-39111000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr19:39110200-39111000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr19:39110200-39111000	Flanking Active TSS	NHLF	lung
45	chr19:39110200-39111000	Flanking Active TSS	Osteobl	bone
46	chr19:39110200-39111200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:39110200-39111200	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
48	chr19:39110200-39111200	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr19:39110400-39110800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39110400-39110800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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