Variant report

Variant	rs9878086
Chromosome Location	chr3:121488353-121488354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121476465..121478394-chr3:121487558..121489191,2	K562	blood:
2	chr3:121480892..121483629-chr3:121486983..121489016,2	K562	blood:
3	chr3:121476185..121478583-chr3:121487333..121489088,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EAF2-2	chr3:121487691-121488674	l_2448_chr3:121487690-121490825_testes

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10934559	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs11706783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714406	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11715951	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716984	0.80[EUR][1000 genomes]
rs11717483	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719458	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11721291	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11721318	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs13061326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065245	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13072618	0.81[EUR][1000 genomes]
rs13072767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074834	0.82[EUR][1000 genomes]
rs13083794	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087578	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs13090798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098883	0.92[ASN][1000 genomes]
rs1318472	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13433692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573819	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17691170	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17742508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1920320	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070180	0.95[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs28660600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28674947	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33988592	0.82[EUR][1000 genomes]
rs34865234	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35359572	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35679661	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988617	0.82[EUR][1000 genomes]
rs3732408	0.82[EUR][1000 genomes]
rs3772128	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3772130	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs3805127	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4280673	0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298081	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4311252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4413346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643643	0.81[EUR][1000 genomes]
rs55657471	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57636696	0.82[AMR][1000 genomes]
rs6768621	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769102	0.86[AMR][1000 genomes]
rs6776670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780302	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784571	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789736	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629369	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7631939	1.00[JPT][hapmap]
rs7649092	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9289177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812137	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816844	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9822949	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825248	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9826473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9839617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848027	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9856641	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9883467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9878086	IQCB1	cis	Whole Blood	GTEx
rs9878086	IQCB1	cis	cerebellum	SCAN
rs9878086	HEG1	cis	parietal	SCAN
rs9878086	EAF2	cis	cerebellum	SCAN
rs9878086	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9878086	IQCB1	cis	parietal	SCAN
rs9878086	PARP9	cis	cerebellum	SCAN
rs9878086	EAF2	cis	lymphoblastoid	seeQTL
rs9878086	SLC15A2	cis	cerebellum	SCAN
rs9878086	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9878086	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs9878086	CHST13	cis	cerebellum	SCAN
rs9878086	HCLS1	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121469400-121489200	Weak transcription	Aorta	Aorta
2	chr3:121469400-121489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:121476800-121489200	Weak transcription	Spleen	Spleen
4	chr3:121477200-121489000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:121477200-121494000	Weak transcription	Right Ventricle	heart
6	chr3:121478000-121499400	Weak transcription	HepG2	liver
7	chr3:121479200-121489200	Weak transcription	HSMMtube	muscle
8	chr3:121480600-121488400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:121482000-121489000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:121482400-121489000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:121482600-121489000	Weak transcription	NH-A	brain
12	chr3:121482600-121489200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:121483200-121488600	Weak transcription	Fetal Brain Female	brain
14	chr3:121483200-121490600	Weak transcription	A549	lung
15	chr3:121483400-121489200	Weak transcription	Esophagus	oesophagus
16	chr3:121483600-121489200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:121483600-121498600	Weak transcription	Fetal Kidney	kidney
18	chr3:121483800-121498400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:121484000-121488600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:121484000-121489000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:121484000-121489200	Weak transcription	Fetal Intestine Small	intestine
22	chr3:121484200-121489000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:121484200-121489200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:121484400-121488800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:121484400-121490600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:121484400-121494000	Weak transcription	Brain Angular Gyrus	brain
27	chr3:121484600-121499000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:121484800-121489000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:121485000-121488600	Weak transcription	Liver	Liver
30	chr3:121485200-121489200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:121485200-121491000	Weak transcription	HUVEC	blood vessel
32	chr3:121485400-121488600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:121485400-121488600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:121485400-121493200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:121485600-121488800	Weak transcription	Osteobl	bone
36	chr3:121485600-121489200	Weak transcription	Fetal Lung	lung
37	chr3:121485600-121497200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:121485600-121503200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:121485800-121488400	Weak transcription	HMEC	breast
40	chr3:121485800-121488600	Weak transcription	Fetal Brain Male	brain
41	chr3:121485800-121488800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:121485800-121501000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:121486000-121488600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:121486000-121488800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:121486000-121489000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:121486000-121489200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:121486000-121489200	Weak transcription	Pancreas	Pancrea
48	chr3:121486000-121489200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:121486000-121489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:121486000-121491400	Weak transcription	NHLF	lung

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