Variant report

Variant	rs12185974
Chromosome Location	chr3:110874481-110874482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1370	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1801650	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1824709	0.89[EUR][1000 genomes]
rs56324569	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56724510	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58112872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61190717	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6437943	0.83[EUR][1000 genomes]
rs73852384	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73852394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852397	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73852401	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73852402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854910	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73854911	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854912	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854914	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854919	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854920	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73854921	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854922	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854923	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73854926	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73854929	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615927	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7616280	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7622397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642664	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9844779	0.83[EUR][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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1008308	chr3:110836281-110885834	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110816000-110893400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:110826800-110884200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:110829400-110893400	Weak transcription	HUVEC	blood vessel
4	chr3:110832200-110881800	Weak transcription	Small Intestine	intestine
5	chr3:110832200-110892400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:110832400-110911200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:110834000-110891800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:110835600-110929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:110838400-110880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:110842600-110911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:110845400-110880000	Weak transcription	Fetal Kidney	kidney
12	chr3:110847000-110911400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:110848200-110891800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:110848400-110879800	Weak transcription	Placenta	Placenta
15	chr3:110853000-110880000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:110853000-110919600	Weak transcription	Fetal Brain Male	brain
17	chr3:110853200-110880200	Weak transcription	Ovary	ovary
18	chr3:110853200-110897000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:110853200-110911000	Weak transcription	NH-A	brain
20	chr3:110853400-110879800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:110857800-110892000	Weak transcription	Adipose Nuclei	Adipose
22	chr3:110860800-110875400	Weak transcription	Fetal Heart	heart
23	chr3:110861800-110880200	Weak transcription	HSMMtube	muscle
24	chr3:110863000-110875600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:110864200-110891800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:110869200-110875000	Strong transcription	Dnd41	blood
27	chr3:110869400-110929000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:110870200-110891800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:110871000-110914200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:110871200-110896400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:110871600-110889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:110871600-110892200	Weak transcription	NHLF	lung
33	chr3:110871800-110878200	Weak transcription	NHDF-Ad	bronchial
34	chr3:110871800-110880000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:110872000-110877600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:110872000-110879800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:110872000-110880200	Weak transcription	Osteobl	bone
38	chr3:110872000-110889800	Weak transcription	Pancreas	Pancrea
39	chr3:110872200-110913800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:110872400-110874800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:110872600-110875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:110872600-110918800	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:110872800-110874800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:110872800-110874800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:110872800-110875000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:110872800-110875000	Strong transcription	Liver	Liver
47	chr3:110872800-110875000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:110872800-110875200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:110872800-110893400	Weak transcription	Gastric	stomach
50	chr3:110872800-110896000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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