Variant report

Variant	rs2439992
Chromosome Location	chr15:76863023-76863024
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs12442966	0.88[EUR][1000 genomes]
rs1443110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs157757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157758	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157760	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs157761	0.87[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs157768	0.93[ASW][hapmap];0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs157769	0.86[CEU][hapmap]
rs157777	0.87[CEU][hapmap]
rs157778	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs157788	0.90[AFR][1000 genomes]
rs157789	0.87[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs166794	0.85[EUR][1000 genomes]
rs182253	0.87[CEU][hapmap]
rs1905694	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs203753	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2078437	0.87[CEU][hapmap]
rs2170998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2439982	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439989	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439991	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454453	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2459360	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2459363	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468113	0.98[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468116	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468120	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2468123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2468129	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469241	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2469242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2469244	0.96[CHD][hapmap];1.00[MEX][hapmap]
rs2585730	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2629021	0.85[EUR][1000 genomes]
rs2629025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs279997	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs279999	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs280005	0.82[EUR][1000 genomes]
rs280008	0.82[EUR][1000 genomes]
rs280012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs280013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs280014	0.85[EUR][1000 genomes]
rs280024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs280028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs280030	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs283796	0.87[CEU][hapmap]
rs283802	0.87[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs284898	0.93[ASW][hapmap];0.87[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap]
rs284902	0.87[CEU][hapmap]
rs284903	0.93[ASW][hapmap];0.87[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap]
rs284904	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs284905	0.87[CEU][hapmap]
rs284907	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap]
rs2930681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2957607	0.87[CEU][hapmap]
rs2957613	0.87[CEU][hapmap]
rs3102710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs35994108	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs387321	0.87[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4886492	0.86[CEU][hapmap]
rs494268	0.87[CEU][hapmap]
rs506000	0.87[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs8031672	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1038233	chr15:76855205-76895763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1037282	chr15:76859309-76895763	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1044453	chr15:76860198-76895763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1620	chr15:76862152-76914288	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
16	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
17	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2439992	SIGLECP3	trans	lymphoblastoid	seeQTL
rs2439992	C15orf60	cis	parietal	SCAN
rs2439992	SCAPER	cis	lymphoblastoid	seeQTL
rs2439992	ISL2	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76846000-76869000	Weak transcription	Left Ventricle	heart
2	chr15:76846000-76869000	Weak transcription	Pancreas	Pancrea
3	chr15:76846200-76868800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:76847000-76868200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:76850200-76868400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:76852000-76867000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr15:76856400-76863800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:76857000-76868800	Weak transcription	Liver	Liver
9	chr15:76858600-76869000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:76860000-76868400	Weak transcription	Esophagus	oesophagus
11	chr15:76861000-76866400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:76861400-76866000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:76861600-76869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:76861800-76863400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:76861800-76869000	Weak transcription	Colonic Mucosa	Colon
16	chr15:76861800-76869000	Weak transcription	Placenta	Placenta
17	chr15:76862400-76863200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:76862400-76864800	Weak transcription	Ovary	ovary
19	chr15:76862600-76864000	Strong transcription	Primary B cells from cord blood	blood
20	chr15:76862600-76868800	Weak transcription	Adipose Nuclei	Adipose
21	chr15:76862600-76869000	Weak transcription	Right Ventricle	heart
22	chr15:76862600-76872000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:76862800-76863600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr15:76862800-76863600	Strong transcription	Dnd41	blood
25	chr15:76862800-76865400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:76863000-76863200	Active TSS	Fetal Brain Male	brain
27	chr15:76863000-76863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:76863000-76864800	Weak transcription	A549	lung
29	chr15:76863000-76865200	Strong transcription	Primary T cells from cord blood	blood
30	chr15:76863000-76865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:76863000-76867400	Weak transcription	Fetal Heart	heart
32	chr15:76863000-76869000	Weak transcription	Fetal Muscle Leg	muscle

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