Variant report

Variant	rs16974093
Chromosome Location	chr19:40650002-40650003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40645584..40647584-chr19:40649751..40651905,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1007628	0.82[JPT][hapmap]
rs10401980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10406471	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10406738	0.84[JPT][hapmap]
rs1327185	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1327187	0.87[ASN][1000 genomes]
rs1327188	0.91[ASN][1000 genomes]
rs1327189	0.92[ASN][1000 genomes]
rs1327190	0.92[ASN][1000 genomes]
rs1327191	0.92[ASN][1000 genomes]
rs1327192	0.92[ASN][1000 genomes]
rs1327193	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13344062	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs163213	0.84[YRI][hapmap]
rs16973950	0.82[JPT][hapmap]
rs170900	0.86[JPT][hapmap]
rs170901	0.85[JPT][hapmap]
rs173061	0.85[JPT][hapmap]
rs17796901	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs17797100	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs183504	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs1854098	0.90[ASN][1000 genomes]
rs186815	0.90[CEU][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1998931	0.92[ASN][1000 genomes]
rs2111543	0.85[JPT][hapmap]
rs2111544	0.85[JPT][hapmap]
rs2231737	0.85[JPT][hapmap]
rs234301	0.85[JPT][hapmap]
rs234302	0.85[JPT][hapmap]
rs234304	0.85[JPT][hapmap]
rs234309	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234318	0.85[JPT][hapmap]
rs234323	0.85[JPT][hapmap]
rs234324	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234325	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234340	0.86[JPT][hapmap]
rs234341	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234352	0.85[JPT][hapmap]
rs234353	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234355	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs234361	0.85[JPT][hapmap]
rs234370	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs234374	0.85[JPT][hapmap]
rs24135	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs24136	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs24137	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2569639	0.92[ASN][1000 genomes]
rs2569640	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2569641	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2569642	0.92[ASN][1000 genomes]
rs2569643	0.90[ASN][1000 genomes]
rs2569644	0.90[ASN][1000 genomes]
rs2569645	0.90[ASN][1000 genomes]
rs2569648	0.90[ASN][1000 genomes]
rs2569649	0.90[ASN][1000 genomes]
rs2569650	0.88[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569651	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2767592	0.90[ASN][1000 genomes]
rs2767593	0.90[ASN][1000 genomes]
rs2767594	0.89[ASN][1000 genomes]
rs2767595	0.90[ASN][1000 genomes]
rs2767596	0.90[ASN][1000 genomes]
rs2767597	0.90[ASN][1000 genomes]
rs2767598	0.90[ASN][1000 genomes]
rs2767601	0.91[ASN][1000 genomes]
rs2767603	0.92[ASN][1000 genomes]
rs2767604	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2767605	0.90[ASN][1000 genomes]
rs2767606	0.90[ASN][1000 genomes]
rs2767607	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2767608	0.90[ASN][1000 genomes]
rs2767609	0.90[ASN][1000 genomes]
rs2819955	0.90[ASN][1000 genomes]
rs2819956	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs2819958	0.92[ASN][1000 genomes]
rs28629274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28890790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915972	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2970102	0.90[ASN][1000 genomes]
rs337779	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs337780	0.86[JPT][hapmap]
rs337784	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337785	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337786	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337787	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337788	0.90[ASN][1000 genomes]
rs337789	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337790	0.90[ASN][1000 genomes]
rs337791	0.89[ASN][1000 genomes]
rs337792	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337793	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs337794	0.92[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs337799	0.90[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs337800	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs337801	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs371500	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs387202	0.85[JPT][hapmap]
rs392958	0.85[JPT][hapmap]
rs421533	0.82[ASW][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs426950	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs4577216	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs459091	0.87[CHD][hapmap]
rs58003479	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58899236	0.90[ASN][1000 genomes]
rs7247527	0.82[JPT][hapmap]
rs73549877	0.89[ASN][1000 genomes]
rs73551642	0.92[ASN][1000 genomes]
rs73551661	0.93[ASN][1000 genomes]
rs73551662	0.93[ASN][1000 genomes]
rs73551663	0.93[ASN][1000 genomes]
rs73551668	0.93[ASN][1000 genomes]
rs73551674	0.93[ASN][1000 genomes]
rs73551675	0.93[ASN][1000 genomes]
rs73551681	0.93[ASN][1000 genomes]
rs73551683	0.92[ASN][1000 genomes]
rs73551685	0.93[ASN][1000 genomes]
rs73551687	0.93[ASN][1000 genomes]
rs73551688	0.93[ASN][1000 genomes]
rs73551689	0.93[ASN][1000 genomes]
rs73551691	0.93[ASN][1000 genomes]
rs73551695	0.92[ASN][1000 genomes]
rs73553603	0.81[ASN][1000 genomes]
rs8103294	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105066	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs8106032	1.00[JPT][hapmap]

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	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
2	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
3	nsv911697	chr19:40599603-40711333	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	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
5	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
6	esv3336591	chr19:40647161-40670363	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16974093	POU2F2	cis	parietal	SCAN
rs16974093	AC005614.5	cis	lung	GTEx
rs16974093	ZNF780A	cis	lung	GTEx
rs16974093	PAFAH1B3	cis	parietal	SCAN
rs16974093	ZNF780A	cis	Thyroid	GTEx
rs16974093	ELSPBP1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40647400-40654400	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:40647800-40654000	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:40648000-40652200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:40648000-40652400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr19:40648000-40654200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:40648200-40654600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr19:40648400-40650200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr19:40648400-40652400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:40648400-40652600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr19:40648600-40650200	Weak transcription	Adipose Nuclei	Adipose
11	chr19:40648600-40653200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:40648600-40653200	Weak transcription	Hela-S3	cervix
13	chr19:40648800-40651200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:40648800-40655000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr19:40649000-40650200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:40649200-40650200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:40649200-40650200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:40649200-40650200	Enhancers	Fetal Brain Male	brain
19	chr19:40649200-40650400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:40649200-40650600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:40649200-40650800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:40649200-40651800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:40649400-40650200	Enhancers	HSMM	muscle
24	chr19:40649400-40650400	Enhancers	HSMMtube	muscle
25	chr19:40649400-40650600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr19:40649400-40651200	Enhancers	Fetal Thymus	thymus
27	chr19:40649600-40650400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr19:40649600-40650400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr19:40649600-40650400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr19:40649600-40650400	Enhancers	Thymus	Thymus
31	chr19:40649600-40651400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:40649600-40653200	Weak transcription	Colonic Mucosa	Colon
33	chr19:40649800-40650200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr19:40649800-40650200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr19:40649800-40650400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:40649800-40650400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr19:40649800-40651200	Weak transcription	Spleen	Spleen
38	chr19:40649800-40651600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr19:40649800-40653200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:40649800-40654400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:40650000-40650200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:40650000-40650200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:40650000-40650400	Flanking Active TSS	GM12878-XiMat	blood
44	chr19:40650000-40650600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links