Variant report

Variant	rs4802919
Chromosome Location	chr19:52798868-52798869
allele	C/G
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	chr19:52771362..52774263-chr19:52797982..52800693,2	K562	blood:
3	chr19:52796840..52799102-chr19:52799281..52802862,3	MCF-7	breast:
4	chr19:52792263..52794621-chr19:52796149..52799005,2	K562	blood:

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

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10402605	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10403158	0.83[ASN][1000 genomes]
rs10404457	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10414779	0.81[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs28405023	0.84[AFR][1000 genomes]
rs28412317	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34016205	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35659666	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4801911	0.83[ASN][1000 genomes]
rs4802917	0.84[AFR][1000 genomes]
rs67621412	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71358869	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4802919	PPP1R12C	cis	cerebellum	SCAN
rs4802919	CDC42EP5	cis	parietal	SCAN
rs4802919	ZBTB45	cis	parietal	SCAN
rs4802919	LILRA1	cis	parietal	SCAN
rs4802919	ZNF548	cis	cerebellum	SCAN
rs4802919	ZNF446	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
2	chr19:52780400-52800000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:52788400-52799800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:52788800-52800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:52789200-52799400	Weak transcription	Pancreas	Pancrea
6	chr19:52791800-52799600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:52792200-52800400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:52794200-52799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:52794400-52799600	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:52794400-52799600	Weak transcription	Esophagus	oesophagus
11	chr19:52794400-52799600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:52794400-52799600	Weak transcription	Stomach Mucosa	stomach
13	chr19:52794400-52799600	Weak transcription	HMEC	breast
14	chr19:52794400-52799600	Weak transcription	NH-A	brain
15	chr19:52794600-52799400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:52794600-52799600	Weak transcription	Primary T cells from cord blood	blood
17	chr19:52794600-52799600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:52794600-52799600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:52794600-52799600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:52794600-52799600	Weak transcription	Brain Anterior Caudate	brain
21	chr19:52794600-52799600	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:52794600-52799600	Weak transcription	Brain Substantia Nigra	brain
23	chr19:52794600-52799600	Weak transcription	Fetal Heart	heart
24	chr19:52794600-52799600	Weak transcription	Fetal Kidney	kidney
25	chr19:52794600-52799600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:52794600-52799600	Weak transcription	HepG2	liver
27	chr19:52794600-52799600	Weak transcription	HUVEC	blood vessel
28	chr19:52794600-52799600	Weak transcription	NHDF-Ad	bronchial
29	chr19:52794600-52799600	Weak transcription	NHEK	skin
30	chr19:52794600-52799800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:52794600-52799800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:52794600-52799800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:52794800-52799400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr19:52794800-52799600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:52794800-52799600	Weak transcription	Primary B cells from cord blood	blood
36	chr19:52794800-52799600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:52794800-52799600	Weak transcription	Fetal Brain Male	brain
38	chr19:52794800-52799600	Weak transcription	Fetal Thymus	thymus
39	chr19:52794800-52799600	Weak transcription	Gastric	stomach
40	chr19:52794800-52799600	Weak transcription	Left Ventricle	heart
41	chr19:52794800-52799600	Weak transcription	Osteobl	bone
42	chr19:52795000-52799600	Weak transcription	Brain Angular Gyrus	brain
43	chr19:52795000-52799600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:52795200-52799600	Weak transcription	Fetal Lung	lung
45	chr19:52795200-52799600	Weak transcription	Right Ventricle	heart
46	chr19:52795400-52799600	Weak transcription	Fetal Brain Female	brain
47	chr19:52795400-52799600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr19:52795600-52799400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr19:52795600-52799600	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:52795800-52799400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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