Variant report

Variant	rs62111460
Chromosome Location	chr19:52827569-52827570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52798639..52802182-chr19:52825182..52828059,3	K562	blood:
2	chr19:52827319..52831915-chr19:52837582..52840953,5	MCF-7	breast:
3	chr19:52822040..52824431-chr19:52826518..52828994,2	K562	blood:
4	chr19:52820318..52821847-chr19:52825066..52827938,2	K562	blood:
5	chr19:52823009..52826195-chr19:52826633..52829397,3	K562	blood:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000167554	Chromatin interaction
ENSG00000269102	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10153516	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2657941	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542592	1.00[ASN][1000 genomes]
rs321927	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55952017	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56014207	0.84[ASN][1000 genomes]
rs56395018	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61309114	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108268	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62110451	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110456	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110457	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62111461	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7359849	1.00[ASN][1000 genomes]
rs8103810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv912299	chr19:52795985-52832830	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
9	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
11	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:52802200-52828400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:52802200-52829200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr19:52802400-52828800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
6	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
7	chr19:52802600-52827600	ZNF genes & repeats	Dnd41	blood
8	chr19:52803800-52829000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
9	chr19:52803800-52829200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:52805200-52829000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr19:52805400-52829200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:52805600-52827800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:52808200-52831800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:52808600-52828000	ZNF genes & repeats	Fetal Lung	lung
15	chr19:52809200-52829800	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr19:52814600-52829400	ZNF genes & repeats	Colon Smooth Muscle	Colon
17	chr19:52814600-52836600	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr19:52814800-52827800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
19	chr19:52814800-52828000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:52814800-52828200	ZNF genes & repeats	A549	lung
21	chr19:52814800-52828400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:52814800-52828800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:52814800-52829200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr19:52814800-52830000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:52814800-52831400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr19:52814800-52831400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:52815000-52827600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
28	chr19:52815000-52827600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr19:52815000-52829200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:52816800-52829200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:52817200-52827600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
32	chr19:52817200-52828400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
33	chr19:52817200-52830200	ZNF genes & repeats	Fetal Brain Female	brain
34	chr19:52817400-52828800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:52817400-52829000	ZNF genes & repeats	Psoas Muscle	Psoas
36	chr19:52818200-52829200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
37	chr19:52818400-52829200	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr19:52818800-52828200	ZNF genes & repeats	Brain Anterior Caudate	brain
39	chr19:52818800-52829200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
40	chr19:52819200-52828000	ZNF genes & repeats	Fetal Kidney	kidney
41	chr19:52819800-52829000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:52820800-52827800	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr19:52821800-52827800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
44	chr19:52821800-52829400	ZNF genes & repeats	Brain Hippocampus Middle	brain
45	chr19:52822200-52828000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
46	chr19:52823600-52828000	ZNF genes & repeats	Right Ventricle	heart
47	chr19:52824000-52828200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr19:52824200-52827600	ZNF genes & repeats	Fetal Heart	heart
49	chr19:52824400-52828000	ZNF genes & repeats	HSMM	muscle
50	chr19:52824400-52828600	Weak transcription	Fetal Stomach	stomach

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