Variant report

Variant	rs16829118
Chromosome Location	chr3:158288822-158288823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10154981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10154986	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1038885	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513527	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12106885	1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12107742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12486595	0.91[EUR][1000 genomes]
rs12487004	0.84[EUR][1000 genomes]
rs12638363	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1320239	0.86[TSI][hapmap]
rs13315529	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13318109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1435638	0.87[EUR][1000 genomes]
rs1435639	0.87[EUR][1000 genomes]
rs16829072	0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs16829079	0.85[TSI][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs16829116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829135	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829273	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16847130	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17630394	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17630785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17631016	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17631078	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864502	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2082838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2115942	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2363657	0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs2364273	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28856044	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806642	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3817373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272617	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4368546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522814	0.85[EUR][1000 genomes]
rs56321207	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56973279	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58034569	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58878998	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59492803	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59502510	0.89[EUR][1000 genomes]
rs59527167	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59602208	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59973861	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61107068	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61292339	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6769314	0.85[TSI][hapmap]
rs6779054	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6788069	0.87[GIH][hapmap]
rs6792976	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795710	0.91[EUR][1000 genomes]
rs6797871	0.90[EUR][1000 genomes]
rs6808551	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73022714	0.89[EUR][1000 genomes]
rs73022726	0.89[EUR][1000 genomes]
rs73022742	0.93[EUR][1000 genomes]
rs73022762	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022770	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73022798	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73024783	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73024790	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73028934	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73030851	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646881	0.87[GIH][hapmap]
rs7646987	0.87[GIH][hapmap]
rs939116	0.84[EUR][1000 genomes]
rs9681065	0.85[TSI][hapmap];0.83[YRI][hapmap]
rs9812307	0.85[TSI][hapmap]
rs9830994	0.87[EUR][1000 genomes]
rs9849437	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9849688	0.85[TSI][hapmap]
rs9864589	0.87[GIH][hapmap]
rs9872682	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881679	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv877690	chr3:158184263-158296916	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv916167	chr3:158240540-158320581	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1013242	chr3:158275578-158305894	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1013112	chr3:158280085-158301728	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1001944	chr3:158280085-158305210	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999408	chr3:158280085-158316431	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3327979	chr3:158288708-158291006	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16829118	MLF1	cis	lymphoblastoid	seeQTL
rs16829118	MLF1	cis	Muscle Skeletal	GTEx
rs16829118	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158288200-158289400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr3:158288200-158289600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:158288200-158290000	Active TSS	Brain Substantia Nigra	brain
4	chr3:158288200-158290200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:158288200-158290600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:158288400-158289000	Active TSS	Duodenum Mucosa	Duodenum
7	chr3:158288400-158289200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:158288400-158289200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:158288400-158289200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:158288400-158289200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:158288400-158289200	ZNF genes & repeats	Fetal Brain Male	brain
12	chr3:158288400-158289200	Active TSS	Ovary	ovary
13	chr3:158288400-158289400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr3:158288400-158289400	Active TSS	Aorta	Aorta
15	chr3:158288400-158289400	Flanking Active TSS	NH-A	brain
16	chr3:158288400-158289600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:158288400-158289600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr3:158288400-158289600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:158288400-158289600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr3:158288400-158289600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr3:158288400-158289600	Active TSS	Psoas Muscle	Psoas
22	chr3:158288400-158289800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:158288400-158290000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr3:158288400-158290000	Active TSS	Brain Germinal Matrix	brain
25	chr3:158288400-158290000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:158288400-158290200	Active TSS	Right Ventricle	heart
27	chr3:158288400-158290400	Active TSS	Fetal Kidney	kidney
28	chr3:158288400-158292000	Active TSS	Right Atrium	heart
29	chr3:158288600-158289000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr3:158288600-158289000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:158288600-158289000	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
32	chr3:158288600-158289000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:158288600-158289000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
34	chr3:158288600-158289000	Active TSS	K562	blood
35	chr3:158288600-158289000	Active TSS	NHLF	lung
36	chr3:158288600-158289200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:158288600-158289200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:158288600-158289200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:158288600-158289200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr3:158288600-158289200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:158288600-158289200	Active TSS	Brain Hippocampus Middle	brain
42	chr3:158288600-158289200	Active TSS	Colonic Mucosa	Colon
43	chr3:158288600-158289200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr3:158288600-158289400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:158288600-158289400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:158288600-158289400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr3:158288600-158289400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:158288600-158289400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr3:158288600-158289400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:158288600-158289400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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