Variant report

Variant	rs1410687
Chromosome Location	chr6:24986163-24986164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10946737	0.85[EUR][1000 genomes]
rs10946739	0.89[EUR][1000 genomes]
rs12192232	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194111	0.88[CEU][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs12205717	0.85[EUR][1000 genomes]
rs1410686	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2149452	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2209932	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2894032	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712870	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4712876	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62401116	0.89[EUR][1000 genomes]
rs6456640	0.88[EUR][1000 genomes]
rs6456641	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6900169	0.86[EUR][1000 genomes]
rs6935286	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742952	0.84[EUR][1000 genomes]
rs7740315	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7768143	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295639	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9295640	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295641	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9358815	0.87[EUR][1000 genomes]
rs9358816	0.84[EUR][1000 genomes]
rs9366591	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9393600	0.96[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1410687	SLC17A2	cis	parietal	SCAN
rs1410687	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24950400-24988600	Weak transcription	Dnd41	blood
2	chr6:24978800-24989400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr6:24979000-24988800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:24980000-24986200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:24980000-24989200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr6:24980200-24990400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:24981200-24991800	Weak transcription	Thymus	Thymus
8	chr6:24981800-24987400	Weak transcription	Lung	lung
9	chr6:24981800-24990600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:24981800-24992000	Weak transcription	Gastric	stomach
11	chr6:24982000-24986400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:24982000-24986600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:24982200-24986600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:24982200-24991800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:24982400-24986400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:24982400-24986600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:24982400-24991800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:24982800-24986400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:24983200-24989600	Weak transcription	Stomach Mucosa	stomach
20	chr6:24984200-24995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:24984800-24986600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr6:24985000-24986400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:24985000-24986400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr6:24985000-24986400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:24985000-24986600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:24985000-24986600	Enhancers	Fetal Heart	heart
27	chr6:24985000-24986800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:24985000-24987000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr6:24985000-24987800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:24985000-24989200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:24985200-24986200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr6:24985200-24986200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:24985200-24986400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:24985200-24986400	Enhancers	HMEC	breast
35	chr6:24985200-24986600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr6:24985200-24986600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:24985200-24986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:24985200-24986800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:24985200-24989000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:24985400-24987000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr6:24985400-24988800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr6:24985600-24987000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:24985600-24987600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:24985600-24989000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:24985800-24989200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr6:24986000-24986200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr6:24986000-24986600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:24986000-24986800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:24986000-24986800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr6:24986000-24987200	Enhancers	Primary T cells from cord blood	blood

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