Variant report

Variant	rs16860849
Chromosome Location	chr3:113049993-113049994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11916690	0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[ASN][1000 genomes]
rs11921931	0.89[ASN][1000 genomes]
rs13064411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065651	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068107	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13083453	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325046	1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.87[ASN][1000 genomes]
rs1386336	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs1486894	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs2018912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087129	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2129434	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs34049435	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34056827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34680203	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278902	0.86[EUR][1000 genomes]
rs35765657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36108475	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773697	0.93[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3829889	0.92[ASN][1000 genomes]
rs55693215	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60131925	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60279293	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61366244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438159	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs66866534	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6773497	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs6783965	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs6787026	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs6798938	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs6799610	0.90[CHD][hapmap];0.96[GIH][hapmap]
rs6808394	0.87[ASN][1000 genomes]
rs7619913	0.92[ASN][1000 genomes]
rs775231	0.93[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860549	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9869119	0.87[ASN][1000 genomes]
rs9869318	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16860849	BOC	cis	cerebellum	SCAN
rs16860849	BOC	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113013600-113065200	Weak transcription	Left Ventricle	heart
2	chr3:113024600-113081000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:113028600-113053400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:113034800-113053600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:113034800-113054000	Weak transcription	Psoas Muscle	Psoas
6	chr3:113035000-113050800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:113035000-113052000	Weak transcription	HSMMtube	muscle
8	chr3:113035000-113053000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:113035400-113052800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:113036400-113053400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:113036400-113055600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:113036600-113051000	Weak transcription	Thymus	Thymus
13	chr3:113036600-113081000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:113036800-113050000	Weak transcription	Right Ventricle	heart
15	chr3:113036800-113050400	Weak transcription	Lung	lung
16	chr3:113036800-113065600	Weak transcription	Aorta	Aorta
17	chr3:113036800-113073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:113036800-113081000	Weak transcription	Gastric	stomach
19	chr3:113036800-113088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:113037000-113053600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:113037800-113065600	Weak transcription	HSMM	muscle
22	chr3:113042000-113080800	Weak transcription	Ovary	ovary
23	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
24	chr3:113042400-113059800	Weak transcription	Pancreas	Pancrea
25	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:113043800-113065600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:113045200-113050600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:113045400-113050000	Weak transcription	Fetal Kidney	kidney
29	chr3:113045400-113050800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:113045400-113051400	Weak transcription	Liver	Liver
31	chr3:113045400-113053000	Weak transcription	Brain Anterior Caudate	brain
32	chr3:113045400-113055400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:113045400-113097600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:113045600-113073000	Weak transcription	A549	lung
35	chr3:113048000-113050200	Strong transcription	Primary T cells from cord blood	blood
36	chr3:113048600-113050600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:113049200-113050000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:113049400-113068400	Weak transcription	Hela-S3	cervix
39	chr3:113049600-113050200	Enhancers	Fetal Muscle Leg	muscle
40	chr3:113049600-113061000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:113049800-113050000	Enhancers	Adipose Nuclei	Adipose
42	chr3:113049800-113050600	Enhancers	Fetal Intestine Large	intestine
43	chr3:113049800-113050600	Enhancers	HepG2	liver

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