Variant report

Variant	rs17796769
Chromosome Location	chr19:40458136-40458137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:166)

rs_ID	r²[population]
rs1007628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10406738	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10417013	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10417043	0.99[ASN][1000 genomes]
rs10418196	0.97[ASN][1000 genomes]
rs11542840	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1327185	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1327193	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs13344062	0.81[ASN][1000 genomes]
rs163213	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16973950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs170901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs173061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17796901	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs17797100	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs183504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186801	0.99[ASN][1000 genomes]
rs186815	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1926931	0.86[ASN][1000 genomes]
rs1926932	0.86[ASN][1000 genomes]
rs1926933	0.86[ASN][1000 genomes]
rs1926934	0.86[ASN][1000 genomes]
rs2111543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2111544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2231737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs234303	0.90[ASN][1000 genomes]
rs234304	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234306	0.94[ASN][1000 genomes]
rs234308	0.95[ASN][1000 genomes]
rs234309	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs234310	0.94[ASN][1000 genomes]
rs234313	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234314	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs234315	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234317	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234318	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234325	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234326	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234328	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234343	0.95[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs234353	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs234355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs234356	0.90[ASN][1000 genomes]
rs234357	0.96[ASN][1000 genomes]
rs234360	0.94[ASN][1000 genomes]
rs234361	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234370	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234371	0.94[ASN][1000 genomes]
rs234374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs24135	0.85[JPT][hapmap]
rs24136	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs24137	0.85[JPT][hapmap]
rs2542303	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2569640	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2569641	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2569650	0.85[JPT][hapmap]
rs2767604	1.00[CEU][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2767607	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2819956	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.99[ASN][1000 genomes]
rs28366011	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915972	1.00[CEU][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs2986595	0.86[ASN][1000 genomes]
rs3000956	0.85[ASN][1000 genomes]
rs337779	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs337784	0.85[JPT][hapmap]
rs337785	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs337786	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs337787	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs337789	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs337792	1.00[CEU][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs337793	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs337794	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs337798	0.83[ASN][1000 genomes]
rs337799	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs337800	0.82[ASN][1000 genomes]
rs34466648	0.91[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs365055	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs371500	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs372599	1.00[ASN][1000 genomes]
rs3760920	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs387202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3887029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs392958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3930885	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs404754	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs416283	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs420579	0.85[ASN][1000 genomes]
rs421533	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs423545	0.96[ASN][1000 genomes]
rs424353	0.94[ASN][1000 genomes]
rs426950	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4577216	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs459091	0.92[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs57219798	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57880771	0.86[ASN][1000 genomes]
rs57900299	0.87[ASN][1000 genomes]
rs58210425	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58284735	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58395013	0.89[ASN][1000 genomes]
rs58440570	0.86[ASN][1000 genomes]
rs58844095	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58941665	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59030876	0.80[ASN][1000 genomes]
rs59502139	0.89[ASN][1000 genomes]
rs59925663	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60080503	0.95[ASN][1000 genomes]
rs60449727	0.87[ASN][1000 genomes]
rs60887294	0.99[ASN][1000 genomes]
rs61236589	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61385499	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615215	0.94[ASN][1000 genomes]
rs7247527	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7257747	0.87[ASN][1000 genomes]
rs7258202	0.87[ASN][1000 genomes]
rs7258506	0.89[ASN][1000 genomes]
rs7258627	0.89[ASN][1000 genomes]
rs7258778	0.87[ASN][1000 genomes]
rs7258974	0.86[ASN][1000 genomes]
rs7259855	0.86[ASN][1000 genomes]
rs7260378	0.86[ASN][1000 genomes]
rs73543974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544000	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73545909	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545911	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73545934	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73545936	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545938	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545945	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545950	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545955	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73545975	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73546001	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73546002	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73547618	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73547620	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73547638	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73547652	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73547656	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73547663	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73547676	0.96[ASN][1000 genomes]
rs73547677	0.96[ASN][1000 genomes]
rs73547696	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73547702	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73549804	0.89[ASN][1000 genomes]
rs73549810	0.89[ASN][1000 genomes]
rs73549811	0.89[ASN][1000 genomes]
rs73549820	0.89[ASN][1000 genomes]
rs73549821	0.83[ASN][1000 genomes]
rs73549825	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73549826	0.86[ASN][1000 genomes]
rs73549829	0.86[ASN][1000 genomes]
rs73549833	0.86[ASN][1000 genomes]
rs73549835	0.86[ASN][1000 genomes]
rs73549836	0.86[ASN][1000 genomes]
rs8105066	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8106032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8108793	0.85[ASN][1000 genomes]
rs9783938	0.83[ASN][1000 genomes]
rs9917073	0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17796769	FCGBP	cis	multi-tissue	Pritchard
rs17796769	FCGBP	cis	lymphoblastoid	seeQTL
rs17796769	ZNF780A	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40450000-40461200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:40450000-40461800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:40450400-40458600	Weak transcription	Thymus	Thymus
4	chr19:40451600-40458800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:40453000-40466000	Weak transcription	Fetal Intestine Small	intestine
6	chr19:40454400-40459200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:40454800-40459000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr19:40454800-40460000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:40455000-40460400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr19:40455800-40458400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
11	chr19:40456000-40460400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:40456400-40459600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr19:40457000-40458200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:40457000-40458400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr19:40457000-40458600	Enhancers	Dnd41	blood
16	chr19:40457000-40458600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
17	chr19:40457200-40458600	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:40457200-40459400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr19:40457200-40460200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:40457400-40458400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:40457400-40458400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:40457400-40475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:40457600-40458400	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr19:40457600-40458400	Flanking Active TSS	Fetal Thymus	thymus
25	chr19:40457600-40459200	Enhancers	GM12878-XiMat	blood
26	chr19:40457600-40459400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr19:40457600-40460000	Enhancers	Stomach Mucosa	stomach
28	chr19:40457600-40460200	Enhancers	Spleen	Spleen
29	chr19:40457800-40458200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr19:40457800-40458400	Enhancers	HMEC	breast
31	chr19:40457800-40459600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr19:40458000-40458200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:40458000-40458200	Flanking Active TSS	A549	lung
34	chr19:40458000-40459200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr19:40458000-40460400	Enhancers	Primary hematopoietic stem cells	blood

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