Variant report

Variant	rs62110400
Chromosome Location	chr19:52780439-52780440
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	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10416641	1.00[ASN][1000 genomes]
rs10422955	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2115077	1.00[ASN][1000 genomes]
rs28718737	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28852381	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56211703	0.81[EUR][1000 genomes]
rs62110397	0.98[EUR][1000 genomes]
rs62110398	0.98[EUR][1000 genomes]
rs62110402	1.00[ASN][1000 genomes]
rs8107325	0.98[EUR][1000 genomes]
rs8113537	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv960862	chr19:52780307-52785546	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
2	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
6	chr19:52774400-52781000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:52774400-52782000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:52774400-52786600	Weak transcription	Osteobl	bone
9	chr19:52774400-52787000	Weak transcription	HUVEC	blood vessel
10	chr19:52774400-52787400	Weak transcription	NHDF-Ad	bronchial
11	chr19:52774600-52781200	ZNF genes & repeats	GM12878-XiMat	blood
12	chr19:52774600-52782000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:52774600-52782600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr19:52774600-52783600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:52774600-52783800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
16	chr19:52774600-52786400	Weak transcription	Brain Angular Gyrus	brain
17	chr19:52774600-52786600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:52774600-52795800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:52774800-52782400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:52774800-52786400	Weak transcription	Brain Substantia Nigra	brain
21	chr19:52775000-52785400	Weak transcription	Gastric	stomach
22	chr19:52775000-52786400	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:52775000-52786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:52775000-52787400	Weak transcription	HepG2	liver
25	chr19:52775200-52786600	Weak transcription	Left Ventricle	heart
26	chr19:52775600-52781800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr19:52775600-52782000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:52776000-52783600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:52776000-52783800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:52776800-52781400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
31	chr19:52777000-52782000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:52777200-52782800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:52777200-52784800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:52777200-52787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:52777200-52794000	Weak transcription	Psoas Muscle	Psoas
36	chr19:52777400-52786400	Weak transcription	Small Intestine	intestine
37	chr19:52777400-52787400	Weak transcription	Fetal Brain Male	brain
38	chr19:52777600-52784800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:52777600-52785400	Weak transcription	Adipose Nuclei	Adipose
40	chr19:52777600-52786000	Weak transcription	NH-A	brain
41	chr19:52777600-52786800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:52777800-52780800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:52777800-52785400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr19:52777800-52785600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:52777800-52785800	Weak transcription	K562	blood
46	chr19:52777800-52786000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:52777800-52786200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:52777800-52786400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:52777800-52786400	Weak transcription	Brain Anterior Caudate	brain
50	chr19:52777800-52786400	Weak transcription	HSMM	muscle

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