Variant report

Variant	rs234301
Chromosome Location	chr19:40522018-40522019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr19:40519569-40522135	U2OS	brain:	n/a	n/a
2	POLR2A	chr19:40519945-40522295	K562	blood:	n/a	n/a
3	POLR2A	chr19:40521969-40523402	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:40517320-40525363	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:40522001-40522085	A549	lung:	n/a	n/a
6	GATA3	chr19:40519564-40522205	A549	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40520246..40523221-chr19:40527503..40530294,2	K562	blood:
2	chr19:40520341..40522642-chr19:40525632..40527204,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF780B-1	chr19:40521102-40522954	NONHSAT066336

No data

Variant related genes	Relation type
ENSG00000268166	TF binding region
ENSG00000268166	Chromatin interaction

Extended variants
information (count: 168 )
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	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10417013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417043	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10418196	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11542840	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1327185	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs1327193	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13344062	0.82[ASN][1000 genomes]
rs163213	0.86[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]
rs170901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs173061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17796769	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17796901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17797100	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs183504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186801	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs186815	0.88[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]
rs1975182	1.00[CEU][hapmap]
rs2111543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs234302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234303	0.91[ASN][1000 genomes]
rs234304	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234306	0.95[ASN][1000 genomes]
rs234308	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs234309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs234310	0.95[ASN][1000 genomes]
rs234313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234314	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs234315	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234317	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234318	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234326	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs234340	0.80[ASN][1000 genomes]
rs234341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][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[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs234356	0.91[ASN][1000 genomes]
rs234357	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs234360	0.95[ASN][1000 genomes]
rs234361	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234370	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs234371	0.95[ASN][1000 genomes]
rs234374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs24135	0.86[JPT][hapmap]
rs24136	0.85[JPT][hapmap]
rs24137	0.86[JPT][hapmap]
rs2542303	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2569640	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2569641	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2569650	0.85[JPT][hapmap]
rs2767604	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2767607	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2819956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28366011	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915972	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs2986595	0.87[ASN][1000 genomes]
rs3000956	0.86[ASN][1000 genomes]
rs337779	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs337784	0.86[JPT][hapmap]
rs337785	1.00[JPT][hapmap]
rs337786	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs337787	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs337789	0.85[JPT][hapmap]
rs337792	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs337793	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs337794	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs337798	0.84[ASN][1000 genomes]
rs337799	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs337800	0.83[ASN][1000 genomes]
rs34466648	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs365055	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371500	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs372599	0.99[ASN][1000 genomes]
rs3760920	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs387202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3887029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs392958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3930885	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404754	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416283	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs420579	0.86[ASN][1000 genomes]
rs421533	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs423545	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs424353	0.95[ASN][1000 genomes]
rs426950	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4577216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs459091	0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs57219798	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57880771	0.87[ASN][1000 genomes]
rs57900299	0.89[ASN][1000 genomes]
rs58210425	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58284735	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58395013	0.90[ASN][1000 genomes]
rs58440570	0.87[ASN][1000 genomes]
rs58844095	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58941665	0.89[EUR][1000 genomes];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	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61385499	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615215	0.95[ASN][1000 genomes]
rs7247527	0.88[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	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73543979	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73544000	0.85[ASN][1000 genomes]
rs73545909	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545911	1.00[ASN][1000 genomes]
rs73545934	1.00[ASN][1000 genomes]
rs73545936	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545938	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545945	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545950	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545955	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73545975	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546001	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73546002	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547618	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547620	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547638	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547652	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73547656	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73547663	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73547676	0.97[ASN][1000 genomes]
rs73547677	0.97[ASN][1000 genomes]
rs73547696	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73547702	0.89[EUR][1000 genomes];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	0.89[EUR][1000 genomes];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	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8106032	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:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs234301	FCGBP	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40504000-40533800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:40512000-40527200	ZNF genes & repeats	Liver	Liver
3	chr19:40513600-40522200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:40514000-40523000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:40515600-40522200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:40517400-40522800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:40517600-40522200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:40517600-40522200	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr19:40517600-40522200	ZNF genes & repeats	Fetal Lung	lung
10	chr19:40517600-40522400	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:40517600-40522400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:40519200-40522200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
13	chr19:40519200-40522400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr19:40519200-40522400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:40519400-40522200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr19:40519600-40522200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr19:40519600-40522400	ZNF genes & repeats	Left Ventricle	heart
18	chr19:40519800-40522200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:40519800-40522400	ZNF genes & repeats	Aorta	Aorta
20	chr19:40521000-40522200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:40521200-40540800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links