Variant report

Variant	rs1410686
Chromosome Location	chr6:24980611-24980612
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24979064..24981330-chr6:25006890..25009589,2	K562	blood:
2	chr6:24980023..24981971-chr6:24983813..24985349,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10946737	0.89[EUR][1000 genomes]
rs10946739	0.82[EUR][1000 genomes]
rs12192232	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194111	0.84[CEU][hapmap];0.83[CHD][hapmap];0.82[EUR][1000 genomes]
rs1410687	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2149452	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2209932	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894032	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712870	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712871	0.87[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712872	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4712876	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62401116	0.82[EUR][1000 genomes]
rs6456640	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6456641	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6900169	0.93[EUR][1000 genomes]
rs6935286	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs742952	0.91[EUR][1000 genomes]
rs7740315	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768143	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774462	0.82[EUR][1000 genomes]
rs9295639	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295640	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295641	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9358815	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9358816	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9366591	0.86[EUR][1000 genomes]
rs9393600	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1410686	ZSCAN16	cis	parietal	SCAN
rs1410686	SLC17A2	cis	parietal	SCAN
rs1410686	HIST1H1A	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24954400-24980800	Weak transcription	Thymus	Thymus
3	chr6:24969200-24980800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:24975400-24980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:24975800-24980800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:24976000-24980800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:24976000-24980800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:24976600-24981600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:24977800-24982000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:24977800-24982400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:24977800-24986000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:24978000-24980800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:24978200-24981000	Weak transcription	Ovary	ovary
14	chr6:24978800-24982000	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:24978800-24989400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr6:24979000-24980800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:24979000-24983400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:24979000-24984200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:24979000-24988800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:24979200-24981800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:24979200-24983200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:24979200-24983200	Enhancers	HSMM	muscle
23	chr6:24979200-24983200	Enhancers	HSMMtube	muscle
24	chr6:24979200-24983400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:24979200-24983600	Enhancers	NHDF-Ad	bronchial
26	chr6:24979200-24983800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:24979200-24984400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:24979400-24980800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:24979400-24981200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:24979400-24981800	Enhancers	Fetal Heart	heart
31	chr6:24979400-24982000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:24979400-24983000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:24979600-24980800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:24979600-24983400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:24979800-24983800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:24980000-24985000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:24980000-24986200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:24980000-24989200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:24980200-24981000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:24980200-24981400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr6:24980200-24983800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:24980200-24990400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:24980400-24981000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:24980400-24983400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:24980600-24980800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:24980600-24982000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr6:24980600-24982000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr6:24980600-24982200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:24980600-24982200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:24980600-24982200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links