Variant report

Variant	rs12976870
Chromosome Location	chr19:53167934-53167935
allele	G/T
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	NFIC	chr19:53166941-53168719	ECC-1	luminal epithelium:	n/a	chr19:53167837-53167865 chr19:53167848-53167865
2	NFIC	chr19:53167021-53168184	ECC-1	luminal epithelium:	n/a	chr19:53167837-53167865 chr19:53167848-53167865
3	POLR2A	chr19:53167622-53167965	K562	blood:	n/a	n/a
4	POLR2A	chr19:53167920-53167967	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:53167690-53167994	K562	blood:	n/a	n/a
6	ZBTB7A	chr19:53167792-53168106	K562	blood:	n/a	n/a
7	POLR2A	chr19:53167700-53167978	K562	blood:	n/a	n/a
8	ELF1	chr19:53167775-53168022	K562	blood:	n/a	n/a
9	EP300	chr19:53167633-53168833	ECC-1	luminal epithelium:	n/a	n/a
10	YY1	chr19:53167776-53167938	K562	blood:	n/a	n/a
11	MAX	chr19:53167717-53168039	K562	blood:	n/a	n/a
12	POLR2A	chr19:53167774-53168031	K562	blood:	n/a	n/a
13	MAZ	chr19:53167748-53168157	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53167030..53169267-chr19:53236508..53239018,2	K562	blood:
2	chr19:53161300..53164636-chr19:53165227..53168992,3	K562	blood:

Variant related genes	Relation type
ZNF83	TF binding region
ENSG00000213020	Chromatin interaction
ENSG00000167766	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11545619	1.00[CEU][hapmap]
rs11880907	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12971911	0.92[EUR][1000 genomes]
rs12974376	1.00[EUR][1000 genomes]
rs12974834	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12981759	0.95[EUR][1000 genomes]
rs13103	0.92[CEU][hapmap]
rs1903703	0.92[EUR][1000 genomes]
rs34570404	1.00[EUR][1000 genomes]
rs34721100	1.00[EUR][1000 genomes]
rs6509661	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71358895	0.92[EUR][1000 genomes]
rs8108275	1.00[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	nsv458744	chr19:53120559-53236331	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS 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	9 gene(s)	inside rSNPs	diseases
16	nsv580028	chr19:53120559-53236331	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
18	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	nsv961238	chr19:53144650-53221094	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
20	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
21	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
22	nsv912319	chr19:53152923-53241107	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv912320	chr19:53164172-53243026	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12976870	ZNF83	Cis_1M	lymphoblastoid	RTeQTL
rs12976870	ZNF83	cis	Whole Blood	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53152200-53172000	Weak transcription	Psoas Muscle	Psoas
2	chr19:53152400-53168600	Strong transcription	Dnd41	blood
3	chr19:53153600-53184200	Weak transcription	Colonic Mucosa	Colon
4	chr19:53154600-53168600	Strong transcription	Fetal Stomach	stomach
5	chr19:53155000-53191400	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:53156200-53168000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:53157000-53176600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:53157200-53168000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr19:53157200-53191600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:53157600-53168400	Weak transcription	HSMMtube	muscle
11	chr19:53158600-53177200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:53158800-53168200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:53158800-53168600	Weak transcription	Fetal Kidney	kidney
14	chr19:53159000-53169400	Weak transcription	Fetal Intestine Large	intestine
15	chr19:53162600-53173200	Weak transcription	Esophagus	oesophagus
16	chr19:53162600-53182600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr19:53162800-53174600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:53162800-53186600	Weak transcription	Aorta	Aorta
19	chr19:53163000-53182600	Weak transcription	Hela-S3	cervix
20	chr19:53163000-53192400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:53163200-53183000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:53163600-53168400	Strong transcription	Thymus	Thymus
23	chr19:53163800-53177200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:53163800-53183200	Weak transcription	HUVEC	blood vessel
25	chr19:53163800-53188400	Weak transcription	Ovary	ovary
26	chr19:53164000-53169000	Weak transcription	Gastric	stomach
27	chr19:53164000-53174400	Weak transcription	GM12878-XiMat	blood
28	chr19:53164000-53178600	Weak transcription	Brain Germinal Matrix	brain
29	chr19:53164000-53183000	Weak transcription	Adipose Nuclei	Adipose
30	chr19:53164000-53185600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:53164000-53192400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:53164000-53192400	Weak transcription	NH-A	brain
33	chr19:53164000-53193000	Weak transcription	Right Ventricle	heart
34	chr19:53164200-53177200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:53164200-53177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:53164200-53192400	Weak transcription	Brain Angular Gyrus	brain
37	chr19:53164400-53176400	Weak transcription	Fetal Lung	lung
38	chr19:53164400-53192400	Weak transcription	HSMM	muscle
39	chr19:53164600-53168200	Weak transcription	Fetal Muscle Leg	muscle
40	chr19:53164600-53168600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:53164600-53189200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:53164600-53192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:53164800-53168600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:53164800-53172800	Weak transcription	Fetal Intestine Small	intestine
45	chr19:53164800-53186400	Weak transcription	Osteobl	bone
46	chr19:53165000-53168400	Weak transcription	Spleen	Spleen
47	chr19:53165000-53177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:53165000-53179000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr19:53165000-53191600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:53165000-53191800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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