Variant report

Variant	rs1019975
Chromosome Location	chr8:103864410-103864411
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	POLR2A	chr8:103864266-103864454	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:103864279-103864577	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr8:103863803-103865382	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:103861529..103864415-chr8:104420889..104423111,2	K562	blood:
2	chr8:103864345..103865888-chr8:103874121..103876056,2	MCF-7	breast:
3	chr8:103864301..103866801-chr8:103868843..103871762,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253385	TF binding region
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10505040	1.00[CHB][hapmap]
rs12544232	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12546193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12546634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546636	0.89[AMR][1000 genomes]
rs12547200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547652	1.00[LWK][hapmap]
rs12548786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512351	1.00[LWK][hapmap]
rs1533182	1.00[LWK][hapmap]
rs17197341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17775390	0.89[AMR][1000 genomes]
rs17775450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17775510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2011262	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2304348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734066	0.89[AMR][1000 genomes]
rs4734670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734674	1.00[LWK][hapmap];0.84[MEX][hapmap]
rs4734676	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4734678	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56854051	0.93[EUR][1000 genomes]
rs62522574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62522576	0.89[AMR][1000 genomes]
rs62522599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526533	0.87[EUR][1000 genomes]
rs62526534	0.85[EUR][1000 genomes]
rs6998032	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap]
rs6999267	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999525	0.87[EUR][1000 genomes]
rs7016840	1.00[JPT][hapmap]
rs7016962	0.86[ASN][1000 genomes]

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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv465751	chr8:103817106-103894326	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv611822	chr8:103817106-103894326	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv891245	chr8:103838004-103907253	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1019975	COX6C	cis	cerebellum	SCAN
rs1019975	AZIN1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103823400-103870600	Weak transcription	Stomach Mucosa	stomach
2	chr8:103826800-103871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:103833400-103870800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:103834600-103867800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr8:103834600-103871200	Strong transcription	K562	blood
6	chr8:103835000-103868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr8:103835000-103871000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr8:103835200-103870200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr8:103835200-103874200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:103835600-103867800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr8:103835800-103871000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr8:103836000-103867800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr8:103836000-103871000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:103836200-103868000	Strong transcription	HMEC	breast
15	chr8:103836200-103873000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:103836600-103870600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr8:103837400-103866400	Strong transcription	NHEK	skin
18	chr8:103837600-103867000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr8:103837600-103870400	Strong transcription	Dnd41	blood
20	chr8:103839200-103870800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr8:103841000-103870200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr8:103843200-103868200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:103843400-103868000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:103845200-103866200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr8:103845600-103868600	Strong transcription	GM12878-XiMat	blood
26	chr8:103847400-103865600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr8:103848800-103869000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:103848800-103870600	Weak transcription	Fetal Heart	heart
29	chr8:103852000-103868800	Weak transcription	Psoas Muscle	Psoas
30	chr8:103853800-103868000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr8:103855200-103870200	Weak transcription	Gastric	stomach
32	chr8:103855400-103866200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:103855400-103870800	Strong transcription	HSMM	muscle
34	chr8:103856000-103871600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr8:103856000-103872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr8:103856000-103874200	Weak transcription	Brain Substantia Nigra	brain
37	chr8:103856200-103873800	Weak transcription	Fetal Brain Male	brain
38	chr8:103856600-103865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr8:103857400-103864800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:103857600-103866200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr8:103857600-103870800	Strong transcription	NH-A	brain
42	chr8:103857800-103868000	Strong transcription	Primary B cells from cord blood	blood
43	chr8:103857800-103871800	Weak transcription	Small Intestine	intestine
44	chr8:103858000-103870200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr8:103858200-103866000	Strong transcription	Primary T cells from cord blood	blood
46	chr8:103858200-103870400	Strong transcription	Fetal Thymus	thymus
47	chr8:103858200-103870600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr8:103858200-103871400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr8:103858400-103866800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr8:103858600-103868000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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