Variant report

Variant	rs12971916
Chromosome Location	chr19:53433054-53433055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53431907..53434266-chr19:53444043..53446544,2	K562	blood:
2	chr19:53425636..53428538-chr19:53430721..53433929,3	K562	blood:

Variant related genes	Relation type
ENSG00000180257	Chromatin interaction
ENSG00000269646	Chromatin interaction
ENSG00000213801	Chromatin interaction
ENSG00000213793	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10402901	1.00[CHB][hapmap]
rs10406237	1.00[CHB][hapmap]
rs10410030	1.00[CHB][hapmap]
rs11084197	1.00[CHB][hapmap]
rs11668258	1.00[CHB][hapmap]
rs12982323	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12982775	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984436	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1661923	1.00[CHB][hapmap]
rs16984438	1.00[CHB][hapmap]
rs16984443	1.00[CHB][hapmap]
rs16984486	1.00[CHB][hapmap]
rs6509725	1.00[CHB][hapmap]
rs71361289	0.88[EUR][1000 genomes]
rs7247568	1.00[CHB][hapmap]
rs7250641	0.99[EUR][1000 genomes]
rs7250706	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102799	1.00[CHB][hapmap]
rs8104237	0.92[EUR][1000 genomes]
rs8104434	0.94[EUR][1000 genomes]
rs8104567	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8109900	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110394	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 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	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
21	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
22	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
23	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
24	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
25	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
26	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
27	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
28	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers 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	30 gene(s)	inside rSNPs	diseases
29	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
30	nsv522421	chr19:53413825-53433054	Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
31	nsv2539	chr19:53428153-53434560	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12971916	TRIM28	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53426600-53444800	Weak transcription	Fetal Heart	heart
2	chr19:53426800-53434200	Weak transcription	NH-A	brain
3	chr19:53426800-53435600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:53426800-53444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:53426800-53445000	Weak transcription	Small Intestine	intestine
6	chr19:53426800-53445200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:53426800-53445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:53427000-53433400	Weak transcription	Lung	lung
9	chr19:53427000-53440200	Weak transcription	Aorta	Aorta
10	chr19:53427000-53442600	Weak transcription	Ovary	ovary
11	chr19:53427000-53444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:53427200-53439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:53427400-53444800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:53427400-53445000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:53427400-53445200	Weak transcription	Left Ventricle	heart
16	chr19:53427600-53434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:53427600-53439600	Weak transcription	Fetal Lung	lung
18	chr19:53427600-53440200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:53427600-53440200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:53427600-53442200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:53427600-53444600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:53427600-53444800	Weak transcription	NHDF-Ad	bronchial
23	chr19:53427800-53434600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:53427800-53434800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:53427800-53437200	Weak transcription	Hela-S3	cervix
26	chr19:53427800-53438200	Weak transcription	Stomach Mucosa	stomach
27	chr19:53427800-53438200	Weak transcription	Osteobl	bone
28	chr19:53427800-53440000	Weak transcription	Colonic Mucosa	Colon
29	chr19:53427800-53440200	Weak transcription	Spleen	Spleen
30	chr19:53427800-53444800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr19:53427800-53445200	Weak transcription	NHLF	lung
32	chr19:53428200-53434200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:53428400-53434000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:53428400-53440400	Weak transcription	NHEK	skin
35	chr19:53428600-53444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:53430200-53434000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr19:53430400-53433800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:53430400-53434400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:53430800-53436800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:53431000-53433200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:53431000-53433200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:53431000-53433400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:53431000-53433800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr19:53431000-53434000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:53431200-53433200	Strong transcription	Primary B cells from cord blood	blood
46	chr19:53431200-53433200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:53431200-53433200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:53431200-53433600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:53431200-53433600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr19:53431200-53433800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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