Variant report

Variant	rs71358869
Chromosome Location	chr19:52797003-52797004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52796840..52799102-chr19:52799281..52802862,3	MCF-7	breast:
3	chr19:52780362..52782762-chr19:52795310..52797361,2	K562	blood:
4	chr19:52792263..52794621-chr19:52796149..52799005,2	K562	blood:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10402605	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10403158	0.95[ASN][1000 genomes]
rs10404457	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10409440	0.90[ASN][1000 genomes]
rs10414779	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28412317	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34016205	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35659666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4801911	0.95[ASN][1000 genomes]
rs4802919	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67621412	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
3	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52785400-52797400	Strong transcription	Brain Germinal Matrix	brain
5	chr19:52788400-52799800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:52788800-52800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:52789200-52799400	Weak transcription	Pancreas	Pancrea
8	chr19:52791800-52799600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:52792200-52800400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:52792600-52797800	ZNF genes & repeats	A549	lung
11	chr19:52794200-52799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:52794400-52799600	Weak transcription	Colon Smooth Muscle	Colon
13	chr19:52794400-52799600	Weak transcription	Esophagus	oesophagus
14	chr19:52794400-52799600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:52794400-52799600	Weak transcription	Stomach Mucosa	stomach
16	chr19:52794400-52799600	Weak transcription	HMEC	breast
17	chr19:52794400-52799600	Weak transcription	NH-A	brain
18	chr19:52794600-52799400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:52794600-52799600	Weak transcription	Primary T cells from cord blood	blood
20	chr19:52794600-52799600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:52794600-52799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:52794600-52799600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:52794600-52799600	Weak transcription	Brain Anterior Caudate	brain
24	chr19:52794600-52799600	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:52794600-52799600	Weak transcription	Brain Substantia Nigra	brain
26	chr19:52794600-52799600	Weak transcription	Fetal Heart	heart
27	chr19:52794600-52799600	Weak transcription	Fetal Kidney	kidney
28	chr19:52794600-52799600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:52794600-52799600	Weak transcription	HepG2	liver
30	chr19:52794600-52799600	Weak transcription	HUVEC	blood vessel
31	chr19:52794600-52799600	Weak transcription	NHDF-Ad	bronchial
32	chr19:52794600-52799600	Weak transcription	NHEK	skin
33	chr19:52794600-52799800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:52794600-52799800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:52794600-52799800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:52794800-52798400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:52794800-52799400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:52794800-52799600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:52794800-52799600	Weak transcription	Primary B cells from cord blood	blood
40	chr19:52794800-52799600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:52794800-52799600	Weak transcription	Fetal Brain Male	brain
42	chr19:52794800-52799600	Weak transcription	Fetal Thymus	thymus
43	chr19:52794800-52799600	Weak transcription	Gastric	stomach
44	chr19:52794800-52799600	Weak transcription	Left Ventricle	heart
45	chr19:52794800-52799600	Weak transcription	Osteobl	bone
46	chr19:52795000-52799600	Weak transcription	Brain Angular Gyrus	brain
47	chr19:52795000-52799600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr19:52795200-52799600	Weak transcription	Fetal Lung	lung
49	chr19:52795200-52799600	Weak transcription	Right Ventricle	heart
50	chr19:52795400-52799600	Weak transcription	Fetal Brain Female	brain

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