Variant report

Variant	rs6684439
Chromosome Location	chr1:154395839-154395840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154395281..154397950-chr1:154401613..154403771,2	K562	blood:
2	chr1:154376615..154383856-chr1:154388009..154396723,15	MCF-7	breast:
3	chr1:154389348..154391422-chr1:154394906..154397857,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11265613	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12118721	0.84[AFR][1000 genomes]
rs12126142	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12730036	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12730935	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12753254	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228145	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4129267	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4133213	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4393147	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453032	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4537545	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4576655	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845372	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845373	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845619	0.87[AFR][1000 genomes]
rs4845620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845621	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845622	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845623	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56383622	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61812598	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6664201	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687726	0.87[AFR][1000 genomes]
rs7512646	0.83[ASN][1000 genomes]
rs7518199	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521458	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7529229	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6684439	LINGO4	cis	parietal	SCAN
rs6684439	HIST2H2AB	cis	cerebellum	SCAN
rs6684439	PYGO2	cis	brain	BrainEAC

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154389200-154397000	Enhancers	Esophagus	oesophagus
4	chr1:154390600-154397400	Enhancers	Brain Angular Gyrus	brain
5	chr1:154390800-154397400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:154390800-154397400	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:154390800-154398000	Enhancers	Placenta	Placenta
8	chr1:154391000-154397200	Enhancers	Brain Substantia Nigra	brain
9	chr1:154391000-154397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:154391400-154397400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:154391600-154399600	Weak transcription	Brain Germinal Matrix	brain
12	chr1:154392400-154396000	Weak transcription	Fetal Kidney	kidney
13	chr1:154392600-154396000	Enhancers	Brain Hippocampus Middle	brain
14	chr1:154392600-154396200	Enhancers	Colon Smooth Muscle	Colon
15	chr1:154392600-154396400	Enhancers	Rectal Smooth Muscle	rectum
16	chr1:154392600-154396600	Weak transcription	Fetal Brain Female	brain
17	chr1:154392600-154397000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:154392600-154397200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:154392800-154396400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:154392800-154396600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:154392800-154396800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:154392800-154397200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:154392800-154397200	Enhancers	Adipose Nuclei	Adipose
24	chr1:154392800-154397200	Enhancers	A549	lung
25	chr1:154392800-154397400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:154392800-154397400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:154392800-154397400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:154392800-154397400	Enhancers	NHDF-Ad	bronchial
29	chr1:154392800-154398000	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:154392800-154398800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:154392800-154399600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:154392800-154400200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:154392800-154400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
35	chr1:154393000-154396200	Weak transcription	Fetal Lung	lung
36	chr1:154393000-154397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr1:154393400-154396600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:154393400-154397000	Enhancers	Psoas Muscle	Psoas
40	chr1:154393600-154396400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:154393600-154396600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:154393800-154396200	Enhancers	NHLF	lung
44	chr1:154393800-154399800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:154393800-154401200	Enhancers	Hela-S3	cervix
46	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:154394000-154396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:154394000-154396600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:154394000-154397000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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