Variant report

Variant	rs11880474
Chromosome Location	chr19:52806312-52806313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52771095..52772682-chr19:52804842..52807560,2	K562	blood:
2	chr19:52804812..52807578-chr19:52808701..52812079,3	MCF-7	breast:
3	chr19:52805604..52808306-chr19:52809399..52811799,3	K562	blood:
4	chr19:52800603..52802220-chr19:52805113..52807077,2	K562	blood:
5	chr19:52799793..52802447-chr19:52803288..52807131,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction

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

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

rs_ID	r²[population]
rs10416012	0.85[CEU][hapmap]
rs11880020	0.90[AFR][1000 genomes]
rs28845817	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs321927	0.85[CEU][hapmap]
rs62110448	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110449	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110450	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6509631	0.85[CEU][hapmap]
rs7253555	0.85[CEU][hapmap]
rs8103072	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8103182	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52801200-52813200	ZNF genes & repeats	A549	lung
2	chr19:52801600-52808800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:52801800-52827200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:52802000-52806400	ZNF genes & repeats	Thymus	Thymus
6	chr19:52802000-52806800	ZNF genes & repeats	GM12878-XiMat	blood
7	chr19:52802000-52808800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:52802000-52813200	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr19:52802000-52826400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:52802200-52808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:52802200-52809000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr19:52802200-52813000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
14	chr19:52802200-52827400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr19:52802200-52828400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:52802200-52829200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr19:52802400-52806800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr19:52802400-52807400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr19:52802400-52808600	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:52802400-52808800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:52802400-52814000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:52802400-52828800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
24	chr19:52802600-52806400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr19:52802600-52826800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:52802600-52827600	ZNF genes & repeats	Dnd41	blood
27	chr19:52802800-52806600	Strong transcription	Psoas Muscle	Psoas
28	chr19:52802800-52808400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:52802800-52809400	Weak transcription	Fetal Heart	heart
30	chr19:52803000-52807000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:52803000-52808000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:52803000-52809200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:52803200-52806600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:52803200-52806800	Strong transcription	Brain Cingulate Gyrus	brain
35	chr19:52803200-52806800	Strong transcription	Fetal Brain Female	brain
36	chr19:52803200-52807000	Strong transcription	Brain Anterior Caudate	brain
37	chr19:52803200-52807000	Strong transcription	Fetal Kidney	kidney
38	chr19:52803200-52807200	Strong transcription	Brain Germinal Matrix	brain
39	chr19:52803200-52812400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:52803400-52806600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
41	chr19:52803400-52806600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:52803400-52806800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
43	chr19:52803400-52807600	Strong transcription	Brain Substantia Nigra	brain
44	chr19:52803400-52807600	Strong transcription	Fetal Brain Male	brain
45	chr19:52803400-52807600	Strong transcription	Fetal Intestine Large	intestine
46	chr19:52803400-52813200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
47	chr19:52803600-52806400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:52803600-52806800	Strong transcription	HUVEC	blood vessel
49	chr19:52803600-52807000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:52803600-52807200	Strong transcription	Brain Hippocampus Middle	brain

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