Variant report

Variant	rs16861059
Chromosome Location	chr3:113211559-113211560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11917869	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11919091	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11919330	0.88[YRI][hapmap]
rs11920233	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11920468	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11920795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11921249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11922003	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11922451	0.85[YRI][hapmap]
rs11924899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11925633	1.00[AMR][1000 genomes]
rs11926656	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11929188	1.00[AMR][1000 genomes]
rs1463639	1.00[YRI][hapmap]
rs16845109	1.00[YRI][hapmap]
rs16845110	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860800	1.00[AMR][1000 genomes]
rs16860854	1.00[AMR][1000 genomes]
rs16860875	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs16860995	1.00[YRI][hapmap]
rs16861014	0.85[YRI][hapmap]
rs16861019	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs16861025	0.88[YRI][hapmap]
rs16861032	0.88[YRI][hapmap]
rs16861045	0.85[YRI][hapmap]
rs16861077	0.88[YRI][hapmap]
rs16861115	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs7430385	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
2	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
3	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
4	chr3:113176400-113233200	Weak transcription	Gastric	stomach
5	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
7	chr3:113179600-113215200	Weak transcription	HMEC	breast
8	chr3:113179600-113217200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:113179600-113232400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:113179600-113232800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
12	chr3:113187200-113224400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:113188000-113215000	Weak transcription	NH-A	brain
14	chr3:113191000-113215200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:113199600-113217000	Weak transcription	Small Intestine	intestine
16	chr3:113201400-113232600	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:113202400-113232800	Weak transcription	Fetal Brain Female	brain
18	chr3:113202600-113211600	Weak transcription	Brain Angular Gyrus	brain
19	chr3:113203200-113223600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:113203400-113229200	Weak transcription	Lung	lung
21	chr3:113203800-113213000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:113204000-113221200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:113204000-113223400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:113204400-113217200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:113204400-113224600	Weak transcription	Aorta	Aorta
26	chr3:113204400-113230600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:113204600-113217200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:113204600-113223000	Weak transcription	HepG2	liver
29	chr3:113204600-113232800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:113204600-113233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:113204600-113233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:113204600-113233200	Weak transcription	Esophagus	oesophagus
33	chr3:113204800-113211600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:113204800-113215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:113204800-113217000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:113204800-113217000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:113204800-113221400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:113204800-113222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:113204800-113232400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:113204800-113232600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:113204800-113232800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:113204800-113233200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:113205000-113211600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:113205000-113216800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:113205000-113224200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:113205000-113224400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:113205200-113220600	Weak transcription	K562	blood
48	chr3:113205400-113212800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:113205800-113212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:113206000-113212400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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