Variant report

Variant	rs234309
Chromosome Location	chr19:40517991-40517992
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 171 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1007628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10406738	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10417013	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10417043	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418196	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11542840	0.99[ASN][1000 genomes]
rs1327185	0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs1327193	0.82[JPT][hapmap]
rs13344062	0.82[ASN][1000 genomes]
rs163213	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16973950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs170900	0.81[CHD][hapmap]
rs170901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs173061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796769	0.99[ASN][1000 genomes]
rs17796901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17797100	0.85[JPT][hapmap]
rs183504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs186801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186815	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1926931	0.87[ASN][1000 genomes]
rs1926932	0.87[ASN][1000 genomes]
rs1926933	0.87[ASN][1000 genomes]
rs1926934	0.87[ASN][1000 genomes]
rs2111543	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2111544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2231737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs234301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234303	0.91[ASN][1000 genomes]
rs234304	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234306	0.95[ASN][1000 genomes]
rs234308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs234310	0.95[ASN][1000 genomes]
rs234313	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234314	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs234315	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234317	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234318	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234324	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234325	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234326	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234328	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234340	0.80[ASN][1000 genomes]
rs234341	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234343	0.94[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs234353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234355	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234356	0.91[ASN][1000 genomes]
rs234357	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234360	0.95[ASN][1000 genomes]
rs234361	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234370	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234371	0.95[ASN][1000 genomes]
rs234374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs24135	0.85[JPT][hapmap]
rs24136	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs24137	0.85[JPT][hapmap]
rs2542303	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2569640	0.85[JPT][hapmap]
rs2569641	0.85[JPT][hapmap]
rs2569650	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2767604	0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs2767607	0.85[JPT][hapmap]
rs2819956	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28366011	1.00[ASN][1000 genomes]
rs2915972	0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs2986595	0.87[ASN][1000 genomes]
rs3000956	0.86[ASN][1000 genomes]
rs337779	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs337784	0.85[JPT][hapmap]
rs337785	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs337786	0.85[JPT][hapmap]
rs337787	0.84[JPT][hapmap]
rs337789	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs337792	0.87[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs337793	0.85[JPT][hapmap]
rs337794	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs337798	0.84[ASN][1000 genomes]
rs337799	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs337800	0.83[ASN][1000 genomes]
rs34466648	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.80[ASN][1000 genomes]
rs365055	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs371500	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs372599	0.99[ASN][1000 genomes]
rs3760920	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs387202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887029	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs392958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3930885	1.00[ASN][1000 genomes]
rs404754	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs416283	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs420579	0.86[ASN][1000 genomes]
rs421533	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs423545	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs424353	0.95[ASN][1000 genomes]
rs426950	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4577216	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs459091	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs57219798	0.99[ASN][1000 genomes]
rs57880771	0.87[ASN][1000 genomes]
rs57900299	0.89[ASN][1000 genomes]
rs58210425	0.92[ASN][1000 genomes]
rs58284735	0.92[ASN][1000 genomes]
rs58395013	0.90[ASN][1000 genomes]
rs58440570	0.87[ASN][1000 genomes]
rs58844095	0.85[ASN][1000 genomes]
rs58941665	0.92[ASN][1000 genomes]
rs59502139	0.90[ASN][1000 genomes]
rs59925663	0.99[ASN][1000 genomes]
rs60080503	0.94[ASN][1000 genomes]
rs60449727	0.89[ASN][1000 genomes]
rs60887294	1.00[ASN][1000 genomes]
rs61236589	1.00[ASN][1000 genomes]
rs61385499	0.97[ASN][1000 genomes]
rs615215	0.95[ASN][1000 genomes]
rs7247527	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7257747	0.88[ASN][1000 genomes]
rs7258202	0.88[ASN][1000 genomes]
rs7258506	0.90[ASN][1000 genomes]
rs7258627	0.90[ASN][1000 genomes]
rs7258778	0.88[ASN][1000 genomes]
rs7258974	0.87[ASN][1000 genomes]
rs7259855	0.87[ASN][1000 genomes]
rs7260378	0.87[ASN][1000 genomes]
rs73543974	0.99[ASN][1000 genomes]
rs73543979	0.99[ASN][1000 genomes]
rs73544000	0.85[ASN][1000 genomes]
rs73545909	1.00[ASN][1000 genomes]
rs73545911	1.00[ASN][1000 genomes]
rs73545934	1.00[ASN][1000 genomes]
rs73545936	1.00[ASN][1000 genomes]
rs73545938	1.00[ASN][1000 genomes]
rs73545945	1.00[ASN][1000 genomes]
rs73545950	1.00[ASN][1000 genomes]
rs73545955	1.00[ASN][1000 genomes]
rs73545975	1.00[ASN][1000 genomes]
rs73546001	1.00[ASN][1000 genomes]
rs73546002	1.00[ASN][1000 genomes]
rs73547618	1.00[ASN][1000 genomes]
rs73547620	1.00[ASN][1000 genomes]
rs73547638	1.00[ASN][1000 genomes]
rs73547652	0.97[ASN][1000 genomes]
rs73547656	0.97[ASN][1000 genomes]
rs73547663	0.97[ASN][1000 genomes]
rs73547676	0.97[ASN][1000 genomes]
rs73547677	0.97[ASN][1000 genomes]
rs73547696	0.92[ASN][1000 genomes]
rs73547702	0.92[ASN][1000 genomes]
rs73549804	0.90[ASN][1000 genomes]
rs73549810	0.90[ASN][1000 genomes]
rs73549811	0.90[ASN][1000 genomes]
rs73549820	0.90[ASN][1000 genomes]
rs73549821	0.84[ASN][1000 genomes]
rs73549825	0.87[ASN][1000 genomes]
rs73549826	0.87[ASN][1000 genomes]
rs73549829	0.87[ASN][1000 genomes]
rs73549833	0.87[ASN][1000 genomes]
rs73549835	0.87[ASN][1000 genomes]
rs73549836	0.87[ASN][1000 genomes]
rs8105066	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8106032	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8108793	0.86[ASN][1000 genomes]
rs9783938	0.84[ASN][1000 genomes]
rs9917073	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs234309	FCGBP	cis	lymphoblastoid	seeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40503600-40519200	Weak transcription	Small Intestine	intestine
2	chr19:40504000-40519600	Weak transcription	Fetal Brain Male	brain
3	chr19:40504000-40519600	Weak transcription	Hela-S3	cervix
4	chr19:40504000-40533800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:40511400-40518000	Strong transcription	Brain Hippocampus Middle	brain
6	chr19:40511600-40522000	ZNF genes & repeats	A549	lung
7	chr19:40511800-40518000	Strong transcription	Colon Smooth Muscle	Colon
8	chr19:40512000-40519200	Strong transcription	Brain Inferior Temporal Lobe	brain
9	chr19:40512000-40527200	ZNF genes & repeats	Liver	Liver
10	chr19:40512200-40518600	Strong transcription	Brain Anterior Caudate	brain
11	chr19:40512600-40518000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:40512600-40519600	Weak transcription	Colonic Mucosa	Colon
13	chr19:40512800-40518200	Strong transcription	Fetal Thymus	thymus
14	chr19:40512800-40518200	Strong transcription	Left Ventricle	heart
15	chr19:40513000-40518400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:40513400-40518800	Strong transcription	Brain Cingulate Gyrus	brain
17	chr19:40513400-40521800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:40513600-40522200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:40513800-40518000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:40513800-40518400	Strong transcription	Brain Angular Gyrus	brain
21	chr19:40514000-40523000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:40514800-40519600	Weak transcription	Right Ventricle	heart
23	chr19:40515000-40518200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:40515000-40519000	Weak transcription	HepG2	liver
25	chr19:40515000-40519400	Weak transcription	Fetal Intestine Large	intestine
26	chr19:40515200-40519200	Weak transcription	HSMMtube	muscle
27	chr19:40515200-40519600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:40515200-40519800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:40515200-40519800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:40515200-40519800	Weak transcription	Pancreas	Pancrea
31	chr19:40515200-40519800	Weak transcription	Thymus	Thymus
32	chr19:40515400-40519000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:40515400-40519000	Weak transcription	NHDF-Ad	bronchial
34	chr19:40515400-40519600	Weak transcription	K562	blood
35	chr19:40515400-40521600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr19:40515600-40519600	Weak transcription	Fetal Heart	heart
37	chr19:40515600-40520000	Weak transcription	Brain Germinal Matrix	brain
38	chr19:40515600-40522200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr19:40516000-40518000	ZNF genes & repeats	Aorta	Aorta
40	chr19:40516000-40518200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:40516000-40518200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr19:40516000-40519200	Weak transcription	Fetal Kidney	kidney
43	chr19:40516000-40519400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:40516000-40519400	Weak transcription	HSMM	muscle
45	chr19:40516000-40519400	Weak transcription	Osteobl	bone
46	chr19:40516000-40519600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr19:40516000-40519600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr19:40516000-40519600	Strong transcription	Dnd41	blood
49	chr19:40516200-40518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:40516200-40519200	Weak transcription	Fetal Brain Female	brain

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