Variant report

Variant	rs234304
Chromosome Location	chr19:40515744-40515745
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	chr19:40514284..40516940-chr19:40519055..40521737,2	K562	blood:

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

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

rs_ID	r²[population]
rs1007628	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10406738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417013	0.95[ASN][1000 genomes]
rs10417043	0.95[ASN][1000 genomes]
rs10418196	0.94[ASN][1000 genomes]
rs11542840	0.94[ASN][1000 genomes]
rs1327185	0.85[JPT][hapmap]
rs1327193	0.85[JPT][hapmap]
rs13344062	0.87[ASN][1000 genomes]
rs163213	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16973950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170901	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs173061	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17796769	0.94[ASN][1000 genomes]
rs17796901	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17797100	0.86[JPT][hapmap]
rs183504	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs186801	0.95[ASN][1000 genomes]
rs186815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1926931	0.83[ASN][1000 genomes]
rs1926932	0.83[ASN][1000 genomes]
rs1926933	0.83[ASN][1000 genomes]
rs1926934	0.83[ASN][1000 genomes]
rs2111543	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2111544	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2231737	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs234301	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234302	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234303	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs234306	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234308	0.91[ASN][1000 genomes]
rs234309	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234313	0.95[ASN][1000 genomes]
rs234314	0.80[ASN][1000 genomes]
rs234315	0.95[ASN][1000 genomes]
rs234317	0.95[ASN][1000 genomes]
rs234318	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234323	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234324	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234325	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234326	0.95[ASN][1000 genomes]
rs234328	0.95[ASN][1000 genomes]
rs234340	0.84[ASN][1000 genomes]
rs234341	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234343	0.99[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs234353	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234355	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs234356	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs234357	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs234360	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234371	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234374	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs24135	0.86[JPT][hapmap]
rs24136	0.85[JPT][hapmap]
rs24137	0.86[JPT][hapmap]
rs2542303	0.95[ASN][1000 genomes]
rs2569640	0.86[JPT][hapmap]
rs2569641	0.86[JPT][hapmap]
rs2569650	0.85[JPT][hapmap]
rs2767604	0.85[JPT][hapmap]
rs2767607	0.85[JPT][hapmap]
rs2819956	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28366011	0.95[ASN][1000 genomes]
rs2915972	0.85[JPT][hapmap]
rs2986595	0.83[ASN][1000 genomes]
rs3000956	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs337784	0.86[JPT][hapmap]
rs337785	1.00[JPT][hapmap]
rs337786	0.86[JPT][hapmap]
rs337787	0.86[JPT][hapmap]
rs337789	0.85[JPT][hapmap]
rs337792	0.85[JPT][hapmap]
rs337793	0.86[JPT][hapmap]
rs337794	1.00[JPT][hapmap]
rs337798	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs337799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs337800	0.88[ASN][1000 genomes]
rs337801	0.85[ASN][1000 genomes]
rs34466648	0.83[CHB][hapmap]
rs365055	0.95[ASN][1000 genomes]
rs371500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372599	0.94[ASN][1000 genomes]
rs3760920	0.83[CHB][hapmap]
rs387202	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3887029	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs392958	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3930885	0.95[ASN][1000 genomes]
rs404754	0.95[ASN][1000 genomes]
rs416283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs420579	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs421533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs423545	0.92[ASN][1000 genomes]
rs424353	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577216	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs459091	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57219798	0.94[ASN][1000 genomes]
rs57880771	0.83[ASN][1000 genomes]
rs57900299	0.84[ASN][1000 genomes]
rs58210425	0.88[ASN][1000 genomes]
rs58284735	0.88[ASN][1000 genomes]
rs58395013	0.85[ASN][1000 genomes]
rs58440570	0.83[ASN][1000 genomes]
rs58844095	0.80[ASN][1000 genomes]
rs58941665	0.88[ASN][1000 genomes]
rs59030876	0.84[ASN][1000 genomes]
rs59502139	0.85[ASN][1000 genomes]
rs59925663	0.94[ASN][1000 genomes]
rs60080503	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60449727	0.84[ASN][1000 genomes]
rs60887294	0.95[ASN][1000 genomes]
rs61236589	0.95[ASN][1000 genomes]
rs61385499	0.92[ASN][1000 genomes]
rs615215	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257747	0.84[ASN][1000 genomes]
rs7258202	0.84[ASN][1000 genomes]
rs7258506	0.85[ASN][1000 genomes]
rs7258627	0.85[ASN][1000 genomes]
rs7258778	0.84[ASN][1000 genomes]
rs7258974	0.83[ASN][1000 genomes]
rs7259855	0.83[ASN][1000 genomes]
rs7260378	0.83[ASN][1000 genomes]
rs73543974	0.94[ASN][1000 genomes]
rs73543979	0.94[ASN][1000 genomes]
rs73544000	0.80[ASN][1000 genomes]
rs73545909	0.95[ASN][1000 genomes]
rs73545911	0.95[ASN][1000 genomes]
rs73545934	0.95[ASN][1000 genomes]
rs73545936	0.95[ASN][1000 genomes]
rs73545938	0.95[ASN][1000 genomes]
rs73545945	0.95[ASN][1000 genomes]
rs73545950	0.95[ASN][1000 genomes]
rs73545955	0.95[ASN][1000 genomes]
rs73545975	0.95[ASN][1000 genomes]
rs73546001	0.95[ASN][1000 genomes]
rs73546002	0.95[ASN][1000 genomes]
rs73547618	0.95[ASN][1000 genomes]
rs73547620	0.95[ASN][1000 genomes]
rs73547638	0.95[ASN][1000 genomes]
rs73547652	0.92[ASN][1000 genomes]
rs73547656	0.92[ASN][1000 genomes]
rs73547663	0.92[ASN][1000 genomes]
rs73547676	0.92[ASN][1000 genomes]
rs73547677	0.92[ASN][1000 genomes]
rs73547696	0.88[ASN][1000 genomes]
rs73547702	0.88[ASN][1000 genomes]
rs73549804	0.85[ASN][1000 genomes]
rs73549810	0.85[ASN][1000 genomes]
rs73549811	0.85[ASN][1000 genomes]
rs73549820	0.85[ASN][1000 genomes]
rs73549825	0.83[ASN][1000 genomes]
rs73549826	0.83[ASN][1000 genomes]
rs73549829	0.83[ASN][1000 genomes]
rs73549833	0.83[ASN][1000 genomes]
rs73549835	0.83[ASN][1000 genomes]
rs73549836	0.83[ASN][1000 genomes]
rs8105066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106032	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8108793	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9783938	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9917073	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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
rs234304	ZNF780A	cis	lung	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40503600-40519200	Weak transcription	Small Intestine	intestine
2	chr19:40503800-40516000	Weak transcription	Fetal Intestine Small	intestine
3	chr19:40504000-40517600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:40504000-40519600	Weak transcription	Fetal Brain Male	brain
5	chr19:40504000-40519600	Weak transcription	Hela-S3	cervix
6	chr19:40504000-40533800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:40511400-40517400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:40511400-40518000	Strong transcription	Brain Hippocampus Middle	brain
9	chr19:40511600-40522000	ZNF genes & repeats	A549	lung
10	chr19:40511800-40516200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:40511800-40516400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:40511800-40518000	Strong transcription	Colon Smooth Muscle	Colon
13	chr19:40512000-40516000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr19:40512000-40517600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr19:40512000-40517800	Strong transcription	Primary B cells from cord blood	blood
16	chr19:40512000-40519200	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr19:40512000-40527200	ZNF genes & repeats	Liver	Liver
18	chr19:40512200-40516400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr19:40512200-40516600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:40512200-40516600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:40512200-40517600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:40512200-40517800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr19:40512200-40518600	Strong transcription	Brain Anterior Caudate	brain
24	chr19:40512400-40515800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:40512400-40516200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:40512400-40516600	Strong transcription	Fetal Lung	lung
27	chr19:40512600-40515800	Weak transcription	NHEK	skin
28	chr19:40512600-40516000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:40512600-40517400	Weak transcription	NH-A	brain
30	chr19:40512600-40518000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:40512600-40519600	Weak transcription	Colonic Mucosa	Colon
32	chr19:40512800-40516000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr19:40512800-40517600	Weak transcription	HUVEC	blood vessel
34	chr19:40512800-40518200	Strong transcription	Fetal Thymus	thymus
35	chr19:40512800-40518200	Strong transcription	Left Ventricle	heart
36	chr19:40513000-40516000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:40513000-40516000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:40513000-40516200	Strong transcription	Placenta	Placenta
39	chr19:40513000-40516600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:40513000-40518400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:40513200-40516600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:40513200-40516600	ZNF genes & repeats	GM12878-XiMat	blood
43	chr19:40513200-40517600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:40513400-40516000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:40513400-40516000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:40513400-40516000	Strong transcription	Osteobl	bone
47	chr19:40513400-40516200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr19:40513400-40518800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr19:40513400-40521800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:40513600-40522200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links