Variant report

Variant	rs4490097
Chromosome Location	chr19:40861724-40861725
allele	A/C
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	PML	chr19:40861607-40862551	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:40861619-40862448	GM12878	blood:	n/a	n/a
3	EBF1	chr19:40861715-40862182	GM12878	blood:	n/a	chr19:40861953-40861964
4	HDAC2	chr19:40861647-40862018	K562	blood:	n/a	n/a
5	ATF2	chr19:40861703-40862360	GM12878	blood:	n/a	n/a
6	RUNX3	chr19:40861588-40862519	GM12878	blood:	n/a	n/a
7	NFIC	chr19:40861714-40862611	GM12878	blood:	n/a	n/a
8	SPI1	chr19:40861636-40862536	GM12878	blood:	n/a	n/a
9	MTA3	chr19:40861547-40862746	GM12878	blood:	n/a	n/a
10	MTA3	chr19:40861572-40862482	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40861491..40863430-chr19:40866543..40869308,2	K562	blood:
2	chr19:40857735..40859819-chr19:40860082..40862864,2	K562	blood:
3	chr19:40858935..40867508-chr19:40870167..40875772,11	K562	blood:

Variant related genes	Relation type
PLD3	TF binding region
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12151335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12460615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16974196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1962639	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1991460	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304186	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs2368575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33933140	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs34894858	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3745195	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3746006	0.81[JPT][hapmap]
rs4479364	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4502340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524046	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802072	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4803324	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803325	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803326	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4803327	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803328	0.85[ASN][1000 genomes]
rs55710016	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57158010	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58502633	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59263025	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7259273	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259541	0.85[JPT][hapmap]
rs73046335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7507651	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7508513	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890773	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs892117	0.82[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4490097	SLC1A5	cis	parietal	SCAN
rs4490097	VASP	cis	cerebellum	SCAN
rs4490097	MIA	cis	lymphoblastoid	seeQTL
rs4490097	DMRTC2	cis	parietal	SCAN
rs4490097	PLAUR	cis	cerebellum	SCAN
rs4490097	TMEM91	cis	parietal	SCAN
rs4490097	ERCC1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40855400-40864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr19:40855600-40861800	Weak transcription	Primary T cells from cord blood	blood
3	chr19:40855600-40861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr19:40855600-40861800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:40855600-40861800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr19:40855600-40861800	Weak transcription	Brain Germinal Matrix	brain
7	chr19:40855600-40861800	Weak transcription	Ovary	ovary
8	chr19:40855600-40861800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr19:40855600-40861800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr19:40855600-40862200	Weak transcription	Adipose Nuclei	Adipose
11	chr19:40855600-40862600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:40855600-40862800	Weak transcription	Brain Anterior Caudate	brain
13	chr19:40855600-40862800	Weak transcription	Fetal Lung	lung
14	chr19:40855600-40863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr19:40855600-40863200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:40855600-40863400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:40855600-40863600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:40855600-40863600	Weak transcription	Fetal Brain Female	brain
19	chr19:40855600-40863800	Weak transcription	Liver	Liver
20	chr19:40855600-40864000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:40855600-40864000	Weak transcription	Spleen	Spleen
22	chr19:40855600-40864000	Weak transcription	NH-A	brain
23	chr19:40855600-40864400	Weak transcription	Placenta	Placenta
24	chr19:40855600-40865200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:40855600-40865200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:40855600-40865200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:40855600-40865200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:40855600-40865200	Weak transcription	Thymus	Thymus
29	chr19:40855600-40865200	Weak transcription	A549	lung
30	chr19:40855600-40865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:40855600-40865400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:40855600-40865400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:40855600-40865800	Weak transcription	K562	blood
34	chr19:40855600-40866000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:40855600-40866200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:40855600-40866200	Weak transcription	Esophagus	oesophagus
37	chr19:40855600-40866600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr19:40855600-40868800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:40855600-40868800	Weak transcription	HSMM	muscle
40	chr19:40855600-40869000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:40855600-40869000	Weak transcription	Osteobl	bone
42	chr19:40855600-40870600	Weak transcription	Gastric	stomach
43	chr19:40855600-40870800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:40855600-40870800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:40855600-40870800	Weak transcription	Hela-S3	cervix
46	chr19:40855600-40871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:40855600-40871000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:40855600-40871000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:40855600-40871000	Weak transcription	Fetal Brain Male	brain
50	chr19:40855600-40871000	Weak transcription	Fetal Intestine Large	intestine

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