Variant report

Variant	rs2303728
Chromosome Location	chr19:41114065-41114066
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr19:41113118-41114286	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41113798-41114271	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:41113315-41114266	K562	blood:	n/a	n/a
4	POLR2A	chr19:41113294-41114391	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:41112960-41114520	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:41113162-41114520	SK-N-MC	brain:	n/a	n/a
7	BRCA1	chr19:41113196-41114164	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr19:41106762-41114701	K562	blood:	n/a	n/a
9	E2F6	chr19:41113130-41114263	Hela-S3	cervix:	n/a	chr19:41114079-41114091
10	POLR2A	chr19:41107105-41114419	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:41113866-41114634	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr19:41112888-41114396	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41031800..41041078-chr19:41106134..41114466,15	K562	blood:
2	chr19:41113914..41116044-chr19:41221538..41224427,3	MCF-7	breast:

Variant related genes	Relation type
RN7SL758P	TF binding region
LTBP4	TF binding region
ENSG00000160460	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10403963	0.80[JPT][hapmap]
rs1051303	0.80[JPT][hapmap]
rs11083560	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2246761	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786527	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802079	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55740667	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55815263	0.91[ASN][1000 genomes]
rs62107907	0.90[ASN][1000 genomes]
rs62107911	0.91[ASN][1000 genomes]
rs62107913	0.95[ASN][1000 genomes]
rs7259237	0.80[JPT][hapmap]
rs7259554	0.80[JPT][hapmap]
rs73047963	0.90[ASN][1000 genomes]
rs73047967	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107014	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
16	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
18	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2303728	CA11	cis	cerebellum	SCAN
rs2303728	DYRK1B	cis	lymphoblastoid	GTEx
rs2303728	QPCTL	cis	cerebellum	SCAN
rs2303728	PGLYRP1	cis	cerebellum	SCAN
rs2303728	SHKBP1	cis	lymphoblastoid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41109800-41122600	Weak transcription	Aorta	Aorta
3	chr19:41110000-41118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41112000-41114200	Bivalent Enhancer	Fetal Stomach	stomach
5	chr19:41112000-41114800	Weak transcription	Fetal Kidney	kidney
6	chr19:41112000-41115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:41112000-41115200	Weak transcription	HUVEC	blood vessel
8	chr19:41112000-41115600	Weak transcription	Brain Angular Gyrus	brain
9	chr19:41112000-41115600	Weak transcription	Brain Anterior Caudate	brain
10	chr19:41112000-41116000	Enhancers	Stomach Mucosa	stomach
11	chr19:41112000-41116200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:41112000-41116200	Weak transcription	NHLF	lung
13	chr19:41112200-41114400	Enhancers	Esophagus	oesophagus
14	chr19:41112200-41115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:41112200-41115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:41112200-41115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:41112200-41115200	Weak transcription	Fetal Lung	lung
18	chr19:41112200-41115200	Weak transcription	Osteobl	bone
19	chr19:41112200-41115400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:41112200-41115400	Weak transcription	Gastric	stomach
21	chr19:41112200-41115400	Weak transcription	Psoas Muscle	Psoas
22	chr19:41112200-41115400	Weak transcription	Small Intestine	intestine
23	chr19:41112200-41115400	Weak transcription	HSMM	muscle
24	chr19:41112400-41114400	Flanking Active TSS	Hela-S3	cervix
25	chr19:41112400-41115000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:41112400-41115000	Weak transcription	GM12878-XiMat	blood
27	chr19:41112400-41115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:41112400-41115200	Enhancers	Primary T cells fromperipheralblood	blood
29	chr19:41112400-41115200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:41112400-41115200	Enhancers	Fetal Intestine Large	intestine
31	chr19:41112600-41114200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:41112600-41114400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:41112600-41114400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:41112600-41114400	Enhancers	A549	lung
35	chr19:41112600-41115000	Enhancers	K562	blood
36	chr19:41112600-41115200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:41112600-41115200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr19:41112600-41115200	Weak transcription	HMEC	breast
39	chr19:41112800-41114400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:41112800-41114400	Bivalent Enhancer	Placenta	Placenta
41	chr19:41112800-41114800	Weak transcription	Primary T cells from cord blood	blood
42	chr19:41112800-41114800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:41112800-41114800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:41112800-41114800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:41113000-41115400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:41113200-41114200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr19:41113200-41114400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr19:41113200-41115400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:41113200-41115400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:41113200-41115400	Enhancers	Skeletal Muscle Male	skeletal muscle

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