Variant report

Variant	rs807479
Chromosome Location	chr19:36253317-36253318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
2	chr19:36249097..36250751-chr19:36253279..36257027,3	K562	blood:
3	chr19:36251835..36255945-chr19:36256071..36258525,4	K562	blood:
4	chr19:36252030..36254335-chr19:36255170..36257529,2	MCF-7	breast:
5	chr19:36247584..36253409-chr19:36264102..36268750,7	K562	blood:

Variant related genes	Relation type
ENSG00000167595	Chromatin interaction
ENSG00000004777	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs107068	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1269214	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs173003	0.82[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs179570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242522	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242523	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285421	0.85[CEU][hapmap]
rs231238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs231244	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs231588	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs231591	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs231592	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55939240	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs614225	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs807478	0.89[EUR][1000 genomes]
rs9917056	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic 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	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs807479	COX6B1	trans	cerebellum	SCAN
rs807479	ZBTB32	cis	Thyroid	GTEx
rs807479	PHLDB3	cis	cerebellum	SCAN
rs807479	AC002398.13	cis	Thyroid	GTEx
rs807479	MEGF8	cis	parietal	SCAN
rs807479	SAMD4B	cis	parietal	SCAN
rs807479	CCDC97	cis	cerebellum	SCAN
rs807479	ZBTB32	cis	lung	GTEx
rs807479	RN7SL765P	cis	Muscle Skeletal	GTEx
rs807479	ZBTB32	cis	Nerve Tibial	GTEx
rs807479	FBXO27	cis	parietal	SCAN
rs807479	UPK1A	trans	cerebellum	SCAN
rs807479	COX6B1	cis	Muscle Skeletal	GTEx
rs807479	COX6B1	trans	parietal	SCAN
rs807479	CEACAM3	cis	cerebellum	SCAN
rs807479	LYPD4	cis	cerebellum	SCAN
rs807479	ZNF568	cis	cerebellum	SCAN
rs807479	COX6B1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36249800-36255000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:36249800-36265600	Weak transcription	Right Atrium	heart
3	chr19:36249800-36265800	Weak transcription	Fetal Kidney	kidney
4	chr19:36250000-36254800	Weak transcription	Adipose Nuclei	Adipose
5	chr19:36250000-36255000	Weak transcription	Esophagus	oesophagus
6	chr19:36250000-36255800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:36250000-36258400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:36250000-36265600	Weak transcription	Brain Substantia Nigra	brain
9	chr19:36250200-36255200	Weak transcription	Primary B cells from cord blood	blood
10	chr19:36250200-36265400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:36250400-36253400	Strong transcription	Fetal Lung	lung
12	chr19:36250400-36255000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:36250400-36260200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:36250400-36265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr19:36250400-36265600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:36250400-36265600	Weak transcription	Psoas Muscle	Psoas
17	chr19:36250400-36265800	Weak transcription	Small Intestine	intestine
18	chr19:36250400-36266000	Weak transcription	Aorta	Aorta
19	chr19:36250600-36253400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:36250600-36254800	Weak transcription	Right Ventricle	heart
21	chr19:36250600-36255000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:36250600-36257400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr19:36250600-36258400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:36250600-36258400	Strong transcription	Fetal Intestine Small	intestine
25	chr19:36250600-36265400	Weak transcription	Stomach Mucosa	stomach
26	chr19:36250800-36254200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr19:36250800-36255000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:36250800-36255800	Weak transcription	HepG2	liver
29	chr19:36250800-36256000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:36250800-36257600	Strong transcription	Fetal Intestine Large	intestine
31	chr19:36250800-36265400	Weak transcription	Brain Angular Gyrus	brain
32	chr19:36250800-36265600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:36251000-36253400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:36251000-36253400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:36251000-36253400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:36251000-36253400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:36251000-36255000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:36251000-36257000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:36251000-36257600	Strong transcription	Primary T cells from cord blood	blood
40	chr19:36251000-36257600	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:36251000-36258400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:36251000-36258400	Strong transcription	Fetal Stomach	stomach
43	chr19:36251000-36260000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:36251000-36260200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:36251000-36260200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:36251000-36263800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:36251000-36265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:36251000-36265600	Weak transcription	Fetal Brain Male	brain
49	chr19:36251000-36265800	Weak transcription	HUVEC	blood vessel
50	chr19:36251000-36266000	Weak transcription	HSMM	muscle

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