Variant report

Variant	rs2304188
Chromosome Location	chr19:40742105-40742106
allele	C/T
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	POLR2A	chr19:40741907-40742341	K562	blood:	n/a	n/a
2	CTCF	chr19:40741303-40742267	A549	lung:	n/a	chr19:40741724-40741737 chr19:40741752-40741765 chr19:40741722-40741740
3	SIN3AK20	chr19:40731136-40743299	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:40739644-40742542	K562	blood:	n/a	n/a
5	POLR2A	chr19:40741774-40742226	K562	blood:	n/a	n/a
6	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a
7	REST	chr19:40740123-40743232	PANC-1	pancreas:	n/a	chr19:40741755-40741768 chr19:40740748-40740756

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40730620..40735723-chr19:40738673..40743679,8	MCF-7	breast:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105219	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10408356	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415181	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416620	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10418932	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10419465	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420842	0.80[ASN][1000 genomes]
rs10422343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs10423896	0.82[ASN][1000 genomes]
rs12151243	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap]
rs16974157	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2163840	0.93[ASN][1000 genomes]
rs28362958	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34716810	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55862427	0.91[ASN][1000 genomes]
rs58336440	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58613082	0.80[ASN][1000 genomes]
rs59010363	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59343080	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59999853	0.81[ASN][1000 genomes]
rs60869669	0.88[ASN][1000 genomes]
rs61685259	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62107590	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62107593	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62107594	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247916	0.87[ASN][1000 genomes]
rs7248861	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7254617	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73044533	0.82[ASN][1000 genomes]
rs8100207	0.87[ASN][1000 genomes]
rs8111619	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8112998	0.87[ASN][1000 genomes]
rs892118	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs892119	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs892120	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304588	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304589	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934426	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1062755	chr19:40737463-40758235	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2304188	DEDD2	cis	cerebellum	SCAN
rs2304188	RPL18	cis	parietal	SCAN
rs2304188	EML2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40732800-40759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:40735600-40757600	Weak transcription	Stomach Mucosa	stomach
3	chr19:40735800-40748200	Weak transcription	Psoas Muscle	Psoas
4	chr19:40737600-40748600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:40737600-40749600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:40737600-40751200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:40738000-40742800	Weak transcription	Fetal Kidney	kidney
8	chr19:40738000-40744200	Strong transcription	Brain Anterior Caudate	brain
9	chr19:40738000-40746600	Strong transcription	Ovary	ovary
10	chr19:40738000-40747000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:40738000-40748600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr19:40738000-40748800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:40738000-40749000	Strong transcription	Thymus	Thymus
14	chr19:40738000-40751600	Strong transcription	Dnd41	blood
15	chr19:40738000-40763800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:40738200-40742800	Weak transcription	NH-A	brain
17	chr19:40738200-40744000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:40738200-40745000	Weak transcription	HSMM	muscle
19	chr19:40738200-40748200	Strong transcription	Pancreas	Pancrea
20	chr19:40738200-40748600	Strong transcription	NHLF	lung
21	chr19:40738200-40748800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:40738200-40749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:40738200-40756200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr19:40738400-40742400	Genic enhancers	Spleen	Spleen
25	chr19:40738400-40745000	Weak transcription	NHDF-Ad	bronchial
26	chr19:40738400-40746800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:40738400-40749400	Strong transcription	Fetal Thymus	thymus
28	chr19:40738400-40749600	Strong transcription	Fetal Brain Female	brain
29	chr19:40738600-40747200	Strong transcription	Brain Cingulate Gyrus	brain
30	chr19:40738600-40747200	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:40738600-40747600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:40738600-40747600	Strong transcription	Lung	lung
33	chr19:40738600-40748600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:40738800-40742800	Weak transcription	Hela-S3	cervix
35	chr19:40738800-40747200	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:40738800-40747600	Weak transcription	Right Atrium	heart
37	chr19:40738800-40748400	Strong transcription	Colonic Mucosa	Colon
38	chr19:40738800-40748600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:40738800-40748800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:40738800-40749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:40738800-40750800	Weak transcription	Fetal Heart	heart
42	chr19:40738800-40758000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr19:40739000-40746400	Strong transcription	Brain Angular Gyrus	brain
44	chr19:40739000-40747400	Strong transcription	Right Ventricle	heart
45	chr19:40739000-40747600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:40739000-40747600	Strong transcription	Brain Germinal Matrix	brain
47	chr19:40739000-40747600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:40739000-40747600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:40739000-40748000	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:40739000-40748600	Strong transcription	Primary monocytes fromperipheralblood	blood

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