Variant report

Variant	rs13345824
Chromosome Location	chr19:53140246-53140247
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53139623..53144311-chr19:53192220..53194807,4	MCF-7	breast:
2	chr19:53140133..53142689-chr19:53604558..53606639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170949	Chromatin interaction
ENSG00000167766	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10406117	0.85[ASN][1000 genomes]
rs10411742	0.85[ASN][1000 genomes]
rs10412842	0.82[ASN][1000 genomes]
rs10418303	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10423447	0.85[ASN][1000 genomes]
rs10423500	0.85[ASN][1000 genomes]
rs10424769	0.85[ASN][1000 genomes]
rs10424979	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12980672	0.85[ASN][1000 genomes]
rs12986098	0.85[ASN][1000 genomes]
rs13345810	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13345832	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126503	0.93[ASN][1000 genomes]
rs34587028	0.93[ASN][1000 genomes]
rs34668321	0.93[ASN][1000 genomes]
rs34764770	0.82[ASN][1000 genomes]
rs35424224	0.93[ASN][1000 genomes]
rs61734108	0.93[ASN][1000 genomes]
rs71358893	0.95[EUR][1000 genomes]
rs71358894	0.95[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	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv1066876	chr19:53123577-53157096	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv580029	chr19:53137583-53164172	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53117800-53140400	Weak transcription	Brain Substantia Nigra	brain
2	chr19:53117800-53140400	Weak transcription	Fetal Heart	heart
3	chr19:53118000-53140400	Weak transcription	Right Ventricle	heart
4	chr19:53121200-53140800	Weak transcription	HSMMtube	muscle
5	chr19:53121400-53140400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:53121400-53140400	Weak transcription	Stomach Mucosa	stomach
7	chr19:53121400-53140400	Weak transcription	NH-A	brain
8	chr19:53121600-53140800	Weak transcription	Brain Angular Gyrus	brain
9	chr19:53122200-53140400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:53123200-53140400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:53123200-53140400	Weak transcription	HMEC	breast
12	chr19:53125000-53140600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:53126200-53140400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:53126200-53140400	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:53126600-53140400	Weak transcription	Pancreas	Pancrea
16	chr19:53126600-53140400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:53127000-53140800	Weak transcription	Ovary	ovary
18	chr19:53129000-53140600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:53129200-53140400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:53129200-53140400	Weak transcription	Fetal Thymus	thymus
21	chr19:53129200-53140600	Weak transcription	Colonic Mucosa	Colon
22	chr19:53129200-53140800	Weak transcription	Small Intestine	intestine
23	chr19:53129600-53140400	Weak transcription	Spleen	Spleen
24	chr19:53129600-53140600	Weak transcription	HSMM	muscle
25	chr19:53129800-53140400	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:53130000-53140600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:53130000-53140800	Weak transcription	Aorta	Aorta
28	chr19:53130400-53140800	Weak transcription	Left Ventricle	heart
29	chr19:53130600-53140400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:53130600-53140400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:53130600-53140400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:53130600-53140800	Weak transcription	Fetal Brain Female	brain
33	chr19:53130600-53140800	Weak transcription	Psoas Muscle	Psoas
34	chr19:53131000-53140400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:53131200-53140400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:53131200-53140600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:53132000-53140400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:53132200-53140600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:53132400-53140400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:53132400-53140400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr19:53132400-53140400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr19:53132600-53140400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:53132600-53140600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:53132800-53140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:53134200-53140600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr19:53135800-53140600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:53137200-53140400	Weak transcription	Placenta	Placenta
48	chr19:53137400-53140400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:53137600-53140600	Weak transcription	Esophagus	oesophagus
50	chr19:53137800-53140800	Weak transcription	Fetal Intestine Large	intestine

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