Variant report

Variant	rs1884945
Chromosome Location	chr6:26533140-26533141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26311628..26314659-chr6:26531812..26534780,3	K562	blood:
2	chr6:26421115..26423072-chr6:26532607..26534934,2	K562	blood:
3	chr6:26532421..26535211-chr6:26570479..26571983,2	MCF-7	breast:
4	chr6:26526578..26530250-chr6:26530283..26533379,3	MCF-7	breast:
5	chr6:26215522..26217770-chr6:26533017..26534753,2	K562	blood:
6	chr6:26531816..26533494-chr6:27804516..27806493,2	K562	blood:
7	chr6:26521199..26522704-chr6:26531334..26533280,2	MCF-7	breast:
8	chr6:26378690..26380275-chr6:26532676..26534577,2	K562	blood:
9	chr6:26526060..26529298-chr6:26530268..26533280,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261353	Chromatin interaction
ENSG00000124549	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000233822	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10447390	0.86[CEU][hapmap]
rs10447391	0.86[CEU][hapmap]
rs10456047	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[MEX][hapmap];1.00[MKK][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]
rs10456331	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807008	1.00[CEU][hapmap]
rs10946820	0.86[CEU][hapmap]
rs10946821	0.86[CEU][hapmap]
rs10946823	0.92[CEU][hapmap]
rs10946824	0.86[CEU][hapmap]
rs10946825	0.91[CEU][hapmap]
rs10946826	0.86[CEU][hapmap]
rs10946827	0.85[CEU][hapmap]
rs10946829	0.86[CEU][hapmap]
rs10946832	1.00[CEU][hapmap]
rs10946842	1.00[JPT][hapmap]
rs1131936	0.93[CEU][hapmap]
rs11753257	1.00[YRI][hapmap]
rs11760103	1.00[YRI][hapmap]
rs12191917	0.86[CEU][hapmap]
rs12193283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194001	0.83[CEU][hapmap]
rs12194036	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12194073	0.86[CEU][hapmap]
rs12196371	1.00[CEU][hapmap]
rs12197304	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198993	0.86[CEU][hapmap]
rs12201546	0.86[CEU][hapmap]
rs12205310	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12206812	0.86[CEU][hapmap]
rs12207930	0.86[CEU][hapmap]
rs12208211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12208272	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208788	0.93[CEU][hapmap]
rs12211872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214444	1.00[CEU][hapmap]
rs12214486	0.86[CEU][hapmap]
rs12214924	0.86[CEU][hapmap]
rs12661560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664899	0.93[CEU][hapmap]
rs17537465	0.93[CEU][hapmap]
rs17539219	0.86[CEU][hapmap]
rs17610161	1.00[CEU][hapmap]
rs17611220	0.86[CEU][hapmap]
rs17611438	0.85[CEU][hapmap]
rs2393652	0.86[CEU][hapmap]
rs2393664	0.81[CEU][hapmap]
rs2893844	0.85[CEU][hapmap]
rs2893845	0.86[CEU][hapmap]
rs2893847	0.86[CEU][hapmap]
rs2893848	0.86[CEU][hapmap]
rs2893849	0.93[CEU][hapmap]
rs2893856	0.93[CEU][hapmap]
rs2893857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3198487	0.85[CEU][hapmap]
rs3208734	0.85[CEU][hapmap]
rs3757143	1.00[YRI][hapmap]
rs3846843	0.86[CEU][hapmap]
rs3846844	0.86[CEU][hapmap]
rs3846847	0.86[CEU][hapmap]
rs3846848	0.86[CEU][hapmap]
rs3846849	0.86[CEU][hapmap]
rs3902051	0.93[CEU][hapmap]
rs4083469	0.86[CEU][hapmap]
rs4609015	0.86[CEU][hapmap]
rs4711108	1.00[CEU][hapmap]
rs4711109	0.86[CEU][hapmap]
rs4711110	1.00[CEU][hapmap]
rs4711111	0.86[CEU][hapmap]
rs4712986	0.93[CEU][hapmap]
rs4712988	0.93[CEU][hapmap]
rs4712990	1.00[CEU][hapmap]
rs4712993	0.86[CEU][hapmap]
rs4712994	0.86[CEU][hapmap]
rs4712996	0.86[CEU][hapmap]
rs4712999	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4713000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713011	1.00[JPT][hapmap]
rs56034653	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6456722	0.85[CEU][hapmap]
rs6456724	0.93[CEU][hapmap]
rs6900725	0.86[CEU][hapmap]
rs6901245	0.84[CEU][hapmap]
rs6910023	0.86[CEU][hapmap]
rs6912934	0.93[CEU][hapmap]
rs6920986	0.86[CEU][hapmap]
rs6926878	0.86[CEU][hapmap]
rs6928454	0.86[CEU][hapmap]
rs6929846	0.86[CEU][hapmap]
rs72843766	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355	0.93[CEU][hapmap]
rs7356849	0.93[CEU][hapmap]
rs7744254	0.86[CEU][hapmap]
rs7745238	0.86[CEU][hapmap]
rs7745767	0.86[CEU][hapmap]
rs7751280	0.86[CEU][hapmap]
rs7768108	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs7770214	0.86[CEU][hapmap]
rs882010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9295690	0.81[CEU][hapmap]
rs9467759	0.93[CEU][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1884945	BTN2A1	cis	parietal	SCAN
rs1884945	OR4K14	trans	parietal	SCAN
rs1884945	ZFYVE9	trans	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26522600-26533200	Weak transcription	NHLF	lung
2	chr6:26522800-26533200	Weak transcription	Ovary	ovary
3	chr6:26523400-26533200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:26523600-26533200	Weak transcription	NHDF-Ad	bronchial
5	chr6:26524000-26533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:26524200-26533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:26526600-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:26528600-26533200	Weak transcription	Psoas Muscle	Psoas
9	chr6:26528800-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:26529200-26533200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:26529400-26533200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:26529600-26533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:26530000-26533200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:26530600-26533200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:26532200-26533200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:26532200-26533200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:26532400-26533200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr6:26532400-26533200	Enhancers	Primary B cells from peripheral blood	blood
19	chr6:26532400-26533200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:26532400-26533200	Weak transcription	Brain Substantia Nigra	brain
21	chr6:26532400-26534000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:26532400-26534000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:26532400-26534000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:26532600-26533200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:26532600-26533200	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:26532600-26533200	Enhancers	A549	lung
27	chr6:26532600-26534000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:26532600-26534000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr6:26532800-26533200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr6:26532800-26533200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:26532800-26533200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:26532800-26533200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:26532800-26533200	Enhancers	Fetal Heart	heart
34	chr6:26532800-26533200	Flanking Active TSS	Dnd41	blood
35	chr6:26532800-26533200	Flanking Active TSS	GM12878-XiMat	blood
36	chr6:26532800-26533200	Enhancers	Hela-S3	cervix
37	chr6:26532800-26533200	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr6:26532800-26533600	Active TSS	Primary B cells from cord blood	blood
39	chr6:26532800-26533800	Active TSS	Aorta	Aorta
40	chr6:26532800-26533800	Flanking Active TSS	Liver	Liver
41	chr6:26532800-26533800	Active TSS	Brain Hippocampus Middle	brain
42	chr6:26532800-26534000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:26532800-26534000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:26532800-26534000	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr6:26532800-26534000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:26532800-26534000	Active TSS	Brain Anterior Caudate	brain
47	chr6:26532800-26534000	Active TSS	Thymus	Thymus
48	chr6:26532800-26534200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:26532800-26534400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:26532800-26535000	Active TSS	HUES6 Cell Line	embryonic stem cell

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