Variant report

Variant	rs3092962
Chromosome Location	chr3:46397039-46397040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46395645..46397767-chr3:46399914..46402472,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1034382	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799865	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2040389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040390	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097282	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2097283	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097284	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2157058	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2187669	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2187670	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2213288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373226	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092963	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3092964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3138042	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34997146	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35510257	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36048784	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36118141	0.80[EUR][1000 genomes]
rs3762823	0.88[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]
rs3918358	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3918359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3918361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276529	0.80[EUR][1000 genomes]
rs4683194	0.80[EUR][1000 genomes]
rs4683199	0.81[EUR][1000 genomes]
rs4683211	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683215	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4683218	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62244813	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6441950	0.80[EUR][1000 genomes]
rs6441958	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441959	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6441960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6441963	0.81[JPT][hapmap]
rs6441968	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441971	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]
rs6441972	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs67450950	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6765031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6785981	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6801761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810232	0.80[EUR][1000 genomes]
rs7371987	0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7432080	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs743660	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7612940	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs762789	0.84[ASN][1000 genomes]
rs7635588	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs768539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839623	0.80[EUR][1000 genomes]
rs9840204	0.80[EUR][1000 genomes]
rs9877860	0.80[EUR][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3092962	SLC26A6	cis	cerebellum	SCAN
rs3092962	SLC25A20	cis	cerebellum	SCAN
rs3092962	CXCR6	cis	parietal	SCAN
rs3092962	DALRD3	cis	cerebellum	SCAN
rs3092962	HIGD1A	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46390200-46397800	Enhancers	Fetal Thymus	thymus
2	chr3:46392400-46402600	Weak transcription	Spleen	Spleen
3	chr3:46394400-46401200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:46395400-46398000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:46395600-46397200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:46395600-46397800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:46395800-46398000	Active TSS	Duodenum Mucosa	Duodenum
8	chr3:46395800-46404200	Weak transcription	Right Atrium	heart
9	chr3:46396000-46397200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:46396000-46397400	Weak transcription	GM12878-XiMat	blood
11	chr3:46396000-46398200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:46396000-46401000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:46396000-46422000	Weak transcription	Lung	lung
14	chr3:46396200-46397400	Weak transcription	Fetal Brain Male	brain
15	chr3:46396200-46398200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:46396200-46398400	Active TSS	Primary T cells fromperipheralblood	blood
17	chr3:46396400-46397600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:46396400-46398600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:46396400-46400800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:46396400-46401000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:46396600-46397400	Enhancers	Primary B cells from cord blood	blood
22	chr3:46396800-46397200	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr3:46396800-46397800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr3:46396800-46401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:46397000-46397200	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr3:46397000-46397200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:46397000-46397400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:46397000-46397400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
29	chr3:46397000-46397600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:46397000-46397600	Bivalent/Poised TSS	Adipose Nuclei	Adipose
31	chr3:46397000-46397600	Weak transcription	Colonic Mucosa	Colon
32	chr3:46397000-46398000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:46397000-46398000	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr3:46397000-46400800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:46397000-46401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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