Variant report

Variant	rs856304
Chromosome Location	chr19:38260910-38260911
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	chr19:38259906..38262114-chr19:38263618..38265240,2	K562	blood:
2	chr19:38259097..38263090-chr19:38267286..38270188,4	K562	blood:

Variant related genes	Relation type
ENSG00000189144	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10048511	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10401968	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10402530	0.82[EUR][1000 genomes]
rs10403173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs10404567	1.00[CEU][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs10408619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10409402	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409487	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420891	0.82[EUR][1000 genomes]
rs11083432	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap]
rs1119229	0.88[CEU][hapmap]
rs11673023	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11878269	0.83[EUR][1000 genomes]
rs11879180	0.82[EUR][1000 genomes]
rs1291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12974225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975057	0.82[EUR][1000 genomes]
rs12979640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs13744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1643466	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs1643467	1.00[CEU][hapmap]
rs1643468	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs16958861	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16958863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs171376	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725499	0.88[CEU][hapmap]
rs1974714	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2075281	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs2075284	0.83[ASN][1000 genomes]
rs2287229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs241932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs241933	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs241950	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909085	0.81[ASN][1000 genomes]
rs2909088	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs2909093	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909100	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2909102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[ASN][1000 genomes]
rs2909105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.81[ASN][1000 genomes]
rs2909109	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs2927739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2927740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap]
rs2927747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2972434	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972445	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972448	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3095724	0.84[ASN][1000 genomes]
rs3095726	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112434	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap]
rs3786869	0.87[CEU][hapmap]
rs3829688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3848626	0.82[EUR][1000 genomes]
rs4239516	0.87[CEU][hapmap]
rs4802135	0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs4803262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4803509	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs6508736	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6508742	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs705495	0.88[CEU][hapmap]
rs7250409	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs7257125	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8101752	0.82[EUR][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs8103633	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8104076	0.83[EUR][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8112706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.82[EUR][1000 genomes]
rs833926	1.00[CEU][hapmap]
rs856300	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304569	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958305	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs968073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs856304	PAFAH1B3	cis	cerebellum	SCAN
rs856304	ZNF571	cis	multi-tissue	Pritchard
rs856304	PHLDB3	cis	parietal	SCAN
rs856304	HIPK4	cis	cerebellum	SCAN
rs856304	DMPK	cis	parietal	SCAN
rs856304	CBLC	cis	parietal	SCAN
rs856304	PHLDB3	cis	cerebellum	SCAN
rs856304	WDR87	cis	Thyroid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
2	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
3	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
4	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
5	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
7	chr19:38248400-38264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:38248800-38269400	Weak transcription	NH-A	brain
9	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
10	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:38250600-38262600	Strong transcription	Stomach Smooth Muscle	stomach
12	chr19:38250600-38264000	Strong transcription	Primary T cells from cord blood	blood
13	chr19:38250600-38264400	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:38250600-38265000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:38250600-38266400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38250800-38261400	Strong transcription	Fetal Stomach	stomach
17	chr19:38251400-38261200	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:38251800-38269400	Weak transcription	Gastric	stomach
19	chr19:38251800-38269400	Weak transcription	HUVEC	blood vessel
20	chr19:38252200-38269400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:38252600-38269000	Weak transcription	NHEK	skin
22	chr19:38253400-38263600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:38253600-38261400	Strong transcription	Fetal Intestine Large	intestine
24	chr19:38253600-38263600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:38254600-38269400	Weak transcription	Right Ventricle	heart
26	chr19:38254800-38269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:38255400-38262600	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:38255400-38264800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr19:38255600-38261000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:38255600-38263000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:38255600-38264000	Strong transcription	Adipose Nuclei	Adipose
32	chr19:38255600-38264200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:38255800-38261200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38255800-38262600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:38255800-38262600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr19:38255800-38265200	Strong transcription	Primary B cells from cord blood	blood
37	chr19:38255800-38266400	ZNF genes & repeats	Liver	Liver
38	chr19:38256000-38262400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:38256000-38262400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:38256400-38262600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:38256400-38263800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr19:38256600-38261400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:38256600-38263000	Strong transcription	Dnd41	blood
44	chr19:38256800-38262400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
45	chr19:38256800-38262600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr19:38256800-38264600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr19:38256800-38269400	Weak transcription	NHLF	lung
48	chr19:38257000-38261200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:38257000-38262000	Weak transcription	Fetal Brain Female	brain
50	chr19:38257000-38262600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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