Variant report

Variant	rs16829840
Chromosome Location	chr3:119147958-119147959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP31-2	chr3:119147387-119149420	NONHSAT091384

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11539377	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11915398	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11916272	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11916344	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11916488	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11917446	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11917642	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11918271	0.90[EUR][1000 genomes]
rs11919404	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11919541	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11919760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11921098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922005	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11923882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925305	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829878	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829888	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3732414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503083	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55696355	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55853418	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55968892	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56149432	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56195264	0.90[EUR][1000 genomes]
rs56413426	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56710033	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57168946	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57389809	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57935532	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58398719	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58639515	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58843212	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58978800	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59482964	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60006470	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6438533	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6762095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763716	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6764495	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6775021	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6776387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6777140	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6779137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802790	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];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808654	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6810215	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs716649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952928	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72952932	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72952934	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72952950	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72970333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72970352	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73857028	0.85[EUR][1000 genomes]
rs7621149	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7626731	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7642119	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7642792	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7650975	0.85[EUR][1000 genomes]
rs7653469	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid)	24823311	GWAS catalog

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119121200-119150000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:119134200-119148800	Weak transcription	Pancreas	Pancrea
3	chr3:119135000-119148000	Weak transcription	Aorta	Aorta
4	chr3:119135200-119149800	Weak transcription	Gastric	stomach
5	chr3:119135400-119148000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:119135400-119150000	Weak transcription	Spleen	Spleen
7	chr3:119138000-119148400	Weak transcription	Fetal Stomach	stomach
8	chr3:119138000-119152400	Weak transcription	Lung	lung
9	chr3:119142400-119150800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:119144400-119150400	ZNF genes & repeats	Liver	Liver
11	chr3:119144600-119152000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:119145400-119148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:119145400-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:119145600-119148000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr3:119145600-119148200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119145600-119149000	ZNF genes & repeats	HSMM	muscle
17	chr3:119145600-119149600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:119145600-119150200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:119145600-119150200	ZNF genes & repeats	Fetal Kidney	kidney
20	chr3:119145600-119152000	ZNF genes & repeats	Fetal Lung	lung
21	chr3:119145800-119150200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr3:119145800-119151000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr3:119145800-119151800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:119146000-119149400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr3:119146200-119149000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
26	chr3:119146400-119150400	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr3:119146400-119150600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:119146400-119150600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr3:119146600-119148400	ZNF genes & repeats	NHDF-Ad	bronchial
30	chr3:119146600-119148600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
31	chr3:119146600-119149400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
32	chr3:119146600-119149400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr3:119146600-119150200	ZNF genes & repeats	A549	lung
34	chr3:119146600-119150600	ZNF genes & repeats	Dnd41	blood
35	chr3:119146600-119151000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:119146800-119148400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr3:119146800-119148800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:119146800-119149400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:119146800-119149400	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr3:119146800-119150000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr3:119147000-119148200	ZNF genes & repeats	NHLF	lung
42	chr3:119147000-119150600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
43	chr3:119147000-119151800	Strong transcription	NH-A	brain
44	chr3:119147000-119152800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:119147000-119179000	Strong transcription	Osteobl	bone
46	chr3:119147200-119148600	ZNF genes & repeats	Fetal Brain Male	brain
47	chr3:119147200-119148600	Weak transcription	HUVEC	blood vessel
48	chr3:119147200-119150400	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr3:119147200-119150400	ZNF genes & repeats	GM12878-XiMat	blood
50	chr3:119147200-119150600	ZNF genes & repeats	Fetal Brain Female	brain

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