Variant report

Variant	rs6509137
Chromosome Location	chr19:44568855-44568856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44568849..44570998-chr19:44573631..44576301,2	K562	blood:
2	chr19:44555194..44558288-chr19:44566078..44569584,3	MCF-7	breast:
3	chr19:44562856..44565736-chr19:44566187..44569653,3	K562	blood:

Variant related genes	Relation type
ENSG00000178386	Chromatin interaction
ENSG00000186026	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11083734	0.83[ASN][1000 genomes]
rs11083735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083736	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11083737	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666432	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610472	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474061	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2138823	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2138824	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2176431	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35120085	0.83[ASN][1000 genomes]
rs382197	0.86[EUR][1000 genomes]
rs3826941	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239528	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427608	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4299256	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4371266	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4444434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451388	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs454904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4550576	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555257	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580302	0.82[ASN][1000 genomes]
rs4803668	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803672	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55798868	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56003307	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56230322	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56250154	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57895932	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62115491	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62119177	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509135	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509139	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251015	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7255192	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257809	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109615	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9646633	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6509137	FUT2	cis	parietal	SCAN
rs6509137	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs6509137	KPTN	cis	parietal	SCAN
rs6509137	ZNF223	cis	Adipose Subcutaneous	GTEx
rs6509137	HIF3A	cis	parietal	SCAN
rs6509137	C19orf73	cis	cerebellum	SCAN
rs6509137	ETFB	cis	parietal	SCAN
rs6509137	ZNF223	cis	Thyroid	GTEx
rs6509137	ASPDH	cis	cerebellum	SCAN
rs6509137	SNORD34	cis	parietal	SCAN
rs6509137	CLPTM1	cis	cerebellum	SCAN
rs6509137	ZNF223	cis	lung	GTEx
rs6509137	APOE	cis	parietal	SCAN
rs6509137	ZNF613	cis	parietal	SCAN
rs6509137	ZNF223	cis	Nerve Tibial	GTEx
rs6509137	OPA3	cis	parietal	SCAN
rs6509137	EMP3	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44557000-44570200	Weak transcription	HUVEC	blood vessel
2	chr19:44557000-44570200	Weak transcription	NHDF-Ad	bronchial
3	chr19:44557000-44575600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:44557400-44570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:44557400-44570200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:44558200-44571800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:44558200-44573200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:44558200-44575600	ZNF genes & repeats	Liver	Liver
9	chr19:44558800-44572800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:44559200-44569000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:44559200-44569000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:44559200-44569400	Strong transcription	Fetal Stomach	stomach
13	chr19:44559400-44569400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:44559400-44570000	Weak transcription	Stomach Mucosa	stomach
15	chr19:44560800-44569400	Strong transcription	Fetal Intestine Large	intestine
16	chr19:44560800-44570000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44561000-44569200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:44561200-44569600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:44561400-44569000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr19:44561400-44570000	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:44561600-44569000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr19:44561600-44569600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:44561800-44569200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:44561800-44569200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:44561800-44569200	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:44561800-44569200	Strong transcription	Placenta	Placenta
27	chr19:44561800-44569600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:44561800-44569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:44561800-44569600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:44561800-44569600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:44561800-44570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:44561800-44570400	Strong transcription	Right Ventricle	heart
33	chr19:44561800-44572000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:44561800-44572600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr19:44562000-44569800	Strong transcription	Brain Germinal Matrix	brain
36	chr19:44562600-44570800	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr19:44563200-44569200	Strong transcription	Fetal Kidney	kidney
38	chr19:44563600-44572200	ZNF genes & repeats	Adipose Nuclei	Adipose
39	chr19:44563800-44570000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:44564400-44569000	Strong transcription	Osteobl	bone
41	chr19:44564400-44569200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:44564600-44569000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:44564600-44569200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:44564600-44569400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:44564800-44570200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:44565000-44569200	Strong transcription	HSMM	muscle
47	chr19:44565400-44569400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:44565600-44572200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr19:44565600-44572200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr19:44566000-44570200	Weak transcription	HepG2	liver

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