Variant report

Variant	rs12972552
Chromosome Location	chr19:42368016-42368017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
2	chr19:42366555..42368141-chr19:42405130..42408050,2	K562	blood:
3	chr19:42367000..42368909-chr19:42375795..42378988,3	MCF-7	breast:
4	chr19:42367135..42368961-chr19:42460272..42462681,2	K562	blood:
5	chr19:42343167..42345193-chr19:42366399..42369039,2	K562	blood:
6	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
7	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
8	chr19:42366833..42368695-chr19:42529044..42531497,2	K562	blood:
9	chr19:42311416..42313552-chr19:42366859..42369350,2	MCF-7	breast:
10	chr19:42366833..42368938-chr19:42528843..42531497,3	K562	blood:
11	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
12	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105404	Chromatin interaction
ENSG00000183103	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000170956	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10415452	0.83[EUR][1000 genomes]
rs28847113	0.80[AMR][1000 genomes]
rs3810153	0.83[EUR][1000 genomes]
rs882520	0.80[EUR][1000 genomes]
rs891167	0.83[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12972552	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs12972552	RABAC1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42364600-42368800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:42364600-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:42364800-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:42365200-42368800	Genic enhancers	Spleen	Spleen
5	chr19:42365200-42369600	Transcr. at gene 5' and 3'	Hela-S3	cervix
6	chr19:42365400-42369200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr19:42365400-42369800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:42365400-42374800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:42365400-42375000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr19:42365600-42368400	Genic enhancers	Brain Cingulate Gyrus	brain
13	chr19:42365600-42368400	Genic enhancers	Stomach Mucosa	stomach
14	chr19:42365600-42368800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:42365600-42368800	Genic enhancers	Gastric	stomach
16	chr19:42365600-42368800	Genic enhancers	Lung	lung
17	chr19:42365600-42369600	Genic enhancers	Pancreas	Pancrea
18	chr19:42365600-42370000	Genic enhancers	Fetal Muscle Leg	muscle
19	chr19:42365600-42370800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:42365600-42374600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:42365600-42374800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr19:42365800-42368800	Genic enhancers	Fetal Stomach	stomach
23	chr19:42365800-42368800	Genic enhancers	Rectal Mucosa Donor 31	rectum
24	chr19:42365800-42368800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr19:42365800-42369000	Strong transcription	Pancreatic Islets	Pancreatic Islet
26	chr19:42365800-42369000	Genic enhancers	Rectal Mucosa Donor 29	rectum
27	chr19:42365800-42369200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:42365800-42369600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:42365800-42370800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:42365800-42374600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr19:42365800-42374800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:42366000-42369000	Genic enhancers	NHDF-Ad	bronchial
34	chr19:42366000-42369200	Genic enhancers	Stomach Smooth Muscle	stomach
35	chr19:42366000-42369600	Strong transcription	Fetal Kidney	kidney
36	chr19:42366000-42370800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:42366000-42374800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
39	chr19:42366200-42368600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:42366200-42369000	Genic enhancers	H1 Cell Line	embryonic stem cell
41	chr19:42366200-42369000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:42366200-42369200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:42366200-42370400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:42366200-42371000	Genic enhancers	Colonic Mucosa	Colon
45	chr19:42366400-42369600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr19:42366400-42369800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr19:42366400-42369800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
49	chr19:42366600-42368400	Weak transcription	Psoas Muscle	Psoas
50	chr19:42366600-42369400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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