Variant report

Variant	rs3760920
Chromosome Location	chr19:40442558-40442559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr19:40441224-40442704	A549	lung:	n/a	chr19:40441429-40441440
2	TCF12	chr19:40440113-40444572	A549	lung:	n/a	chr19:40442444-40442454 chr19:40442130-40442140 chr19:40442317-40442326 chr19:40440845-40440855 chr19:40441092-40441102
3	FOXA2	chr19:40441728-40442752	A549	lung:	n/a	n/a
4	REST	chr19:40441644-40442612	A549	lung:	n/a	chr19:40442131-40442149 chr19:40441950-40441968 chr19:40442205-40442223 chr19:40442130-40442143 chr19:40442133-40442146 chr19:40442204-40442224 chr19:40441732-40441746
5	FOXA2	chr19:40441733-40442712	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40441756..40443271-chr19:40480700..40482309,2	K562	blood:

Variant related genes	Relation type
FCGBP	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1007628	0.91[CHB][hapmap]
rs10406738	0.91[CHB][hapmap]
rs10417013	0.84[ASN][1000 genomes]
rs10417043	0.84[ASN][1000 genomes]
rs10418196	0.82[ASN][1000 genomes]
rs11542840	0.82[ASN][1000 genomes]
rs163213	0.91[CHB][hapmap]
rs16973950	0.90[CHB][hapmap]
rs170901	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs173061	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs17796769	0.85[ASN][1000 genomes]
rs17796901	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs183504	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[ASN][1000 genomes]
rs186801	0.84[ASN][1000 genomes]
rs186815	0.83[CHB][hapmap]
rs2111543	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2111544	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2231737	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs234301	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs234302	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs234304	0.83[CHB][hapmap]
rs234308	0.80[ASN][1000 genomes]
rs234309	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs234313	0.84[ASN][1000 genomes]
rs234315	0.84[ASN][1000 genomes]
rs234317	0.84[ASN][1000 genomes]
rs234318	0.83[CHB][hapmap]
rs234323	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs234324	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs234325	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs234326	0.84[ASN][1000 genomes]
rs234328	0.84[ASN][1000 genomes]
rs234341	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs234343	0.80[ASN][1000 genomes]
rs234352	1.00[CHB][hapmap]
rs234353	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs234355	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs234357	0.81[ASN][1000 genomes]
rs234361	0.83[CHB][hapmap]
rs234370	0.83[CHB][hapmap]
rs234374	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs2542303	0.84[ASN][1000 genomes]
rs2819956	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[ASN][1000 genomes]
rs28366011	0.84[ASN][1000 genomes]
rs337779	0.83[CHB][hapmap]
rs337785	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs337786	0.83[CHB][hapmap]
rs337799	0.83[CHB][hapmap]
rs34466648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs365055	0.84[ASN][1000 genomes]
rs371500	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs372599	0.85[ASN][1000 genomes]
rs3760919	0.83[YRI][hapmap]
rs387202	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs3887029	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs392958	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3930885	0.84[ASN][1000 genomes]
rs404754	0.84[ASN][1000 genomes]
rs416283	0.83[CHB][hapmap]
rs421533	0.83[CHB][hapmap]
rs423545	0.81[ASN][1000 genomes]
rs426950	0.83[CHB][hapmap]
rs4577216	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap]
rs459091	0.83[CHB][hapmap]
rs57219798	0.85[ASN][1000 genomes]
rs59925663	0.85[ASN][1000 genomes]
rs60080503	0.80[ASN][1000 genomes]
rs60887294	0.84[ASN][1000 genomes]
rs61236589	0.84[ASN][1000 genomes]
rs61385499	0.81[ASN][1000 genomes]
rs7247527	0.83[CHB][hapmap]
rs73543974	0.85[ASN][1000 genomes]
rs73543979	0.85[ASN][1000 genomes]
rs73545909	0.84[ASN][1000 genomes]
rs73545911	0.84[ASN][1000 genomes]
rs73545934	0.84[ASN][1000 genomes]
rs73545936	0.84[ASN][1000 genomes]
rs73545938	0.84[ASN][1000 genomes]
rs73545945	0.84[ASN][1000 genomes]
rs73545950	0.84[ASN][1000 genomes]
rs73545955	0.84[ASN][1000 genomes]
rs73545975	0.84[ASN][1000 genomes]
rs73546001	0.84[ASN][1000 genomes]
rs73546002	0.84[ASN][1000 genomes]
rs73547618	0.84[ASN][1000 genomes]
rs73547620	0.84[ASN][1000 genomes]
rs73547638	0.84[ASN][1000 genomes]
rs73547652	0.81[ASN][1000 genomes]
rs73547656	0.81[ASN][1000 genomes]
rs73547663	0.81[ASN][1000 genomes]
rs73547676	0.81[ASN][1000 genomes]
rs73547677	0.81[ASN][1000 genomes]
rs8105066	0.83[CHB][hapmap]
rs8106032	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	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
rs3760920	SERTAD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40438600-40443800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr19:40439800-40443800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr19:40439800-40443800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:40439800-40443800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr19:40439800-40444600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr19:40440000-40443800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:40440000-40443800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr19:40440000-40444000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:40440000-40444000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr19:40440000-40444200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:40440000-40444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:40440200-40443800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr19:40440400-40443600	Enhancers	Spleen	Spleen
14	chr19:40440400-40443800	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:40440600-40442600	Bivalent Enhancer	Placenta	Placenta
16	chr19:40440600-40442800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr19:40440600-40443800	Enhancers	Primary T cells from cord blood	blood
18	chr19:40440600-40443800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:40440600-40444000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr19:40440800-40443000	Enhancers	Primary B cells from cord blood	blood
21	chr19:40440800-40443600	Enhancers	Colonic Mucosa	Colon
22	chr19:40440800-40443800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:40440800-40444000	Enhancers	Fetal Intestine Small	intestine
24	chr19:40440800-40444600	Enhancers	Fetal Intestine Large	intestine
25	chr19:40440800-40447000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:40441000-40443000	Enhancers	Duodenum Mucosa	Duodenum
27	chr19:40441000-40443200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
28	chr19:40441000-40443800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr19:40441000-40443800	Enhancers	GM12878-XiMat	blood
30	chr19:40441200-40449000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:40441400-40442600	Flanking Active TSS	A549	lung
32	chr19:40441600-40443600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr19:40441600-40443600	Enhancers	Fetal Thymus	thymus
34	chr19:40441800-40443200	Bivalent Enhancer	Adipose Nuclei	Adipose
35	chr19:40441800-40444200	Enhancers	Stomach Mucosa	stomach
36	chr19:40441800-40447200	Weak transcription	Esophagus	oesophagus
37	chr19:40442000-40446400	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:40442000-40450400	Weak transcription	Brain Substantia Nigra	brain
39	chr19:40442200-40442600	Enhancers	Small Intestine	intestine
40	chr19:40442200-40443200	Weak transcription	Fetal Muscle Leg	muscle
41	chr19:40442200-40443600	Enhancers	Fetal Muscle Trunk	muscle
42	chr19:40442200-40444400	Enhancers	HepG2	liver
43	chr19:40442200-40447000	Weak transcription	Gastric	stomach
44	chr19:40442400-40442600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr19:40442400-40442800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:40442400-40449000	Weak transcription	Pancreas	Pancrea
47	chr19:40442400-40450400	Weak transcription	Lung	lung

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