Variant report

Variant	rs12971612
Chromosome Location	chr19:53405460-53405461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53400554..53402197-chr19:53402529..53405491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182986	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10401230	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343389	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690522	0.80[EUR][1000 genomes]
rs8102523	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104476	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106242	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
16	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv458747	chr19:53302481-53424324	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
21	nsv580034	chr19:53302481-53424324	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
22	nsv912329	chr19:53317001-53440653	Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
23	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
24	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
25	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
26	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
27	nsv912340	chr19:53370345-53430362	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
28	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
29	esv3392897	chr19:53389142-53418469	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12971612	ZNF615	cis	Nerve Tibial	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53401000-53407200	Weak transcription	Gastric	stomach
2	chr19:53401000-53425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:53401200-53409800	Weak transcription	Small Intestine	intestine
4	chr19:53401400-53408800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:53401400-53409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:53401400-53409200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:53401400-53409200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:53401400-53409200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:53401400-53409200	Weak transcription	Ovary	ovary
10	chr19:53401400-53409200	Weak transcription	NH-A	brain
11	chr19:53401400-53409400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:53401400-53409400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:53401400-53409400	Weak transcription	Fetal Lung	lung
14	chr19:53401400-53409400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:53401400-53410400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr19:53401400-53410600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:53401400-53410600	Weak transcription	Aorta	Aorta
18	chr19:53401400-53410600	Weak transcription	HUVEC	blood vessel
19	chr19:53401400-53411800	Weak transcription	Fetal Intestine Small	intestine
20	chr19:53401400-53425600	Weak transcription	NHDF-Ad	bronchial
21	chr19:53401400-53425800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr19:53401600-53406400	Weak transcription	Fetal Kidney	kidney
23	chr19:53401600-53407000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:53401600-53407200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:53401600-53407400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr19:53401600-53408800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:53401600-53409200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:53401600-53409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:53401600-53409200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:53401600-53409200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:53401600-53409400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:53401600-53409400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:53401600-53409400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:53401600-53409400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:53401600-53409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr19:53401600-53409400	Weak transcription	Fetal Intestine Large	intestine
37	chr19:53401600-53409400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:53401600-53409400	Weak transcription	K562	blood
39	chr19:53401600-53409800	Weak transcription	HSMM	muscle
40	chr19:53401600-53410000	Weak transcription	Thymus	Thymus
41	chr19:53401600-53410200	Weak transcription	Osteobl	bone
42	chr19:53401600-53410400	Weak transcription	Colonic Mucosa	Colon
43	chr19:53401600-53410400	Weak transcription	Spleen	Spleen
44	chr19:53401600-53411200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:53401600-53412200	Weak transcription	Psoas Muscle	Psoas
46	chr19:53401600-53413200	Weak transcription	HSMMtube	muscle
47	chr19:53401600-53419000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:53401600-53419200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:53401600-53425600	Weak transcription	Brain Hippocampus Middle	brain
50	chr19:53401600-53425600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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