Variant report

Variant	rs828606
Chromosome Location	chr3:98525513-98525514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98523635-98529478	U87	brain:	n/a	n/a
2	POLR2A	chr3:98523592-98529440	U87	brain:	n/a	n/a
3	POLR2A	chr3:98523586-98529440	U87	brain:	n/a	n/a
4	POLR2A	chr3:98525291-98525861	HCT-116	colon:	n/a	n/a
5	POLR2A	chr3:98523621-98529478	U87	brain:	n/a	n/a
6	POLR2A	chr3:98525157-98525836	HCT-116	colon:	n/a	n/a
7	POLR2A	chr3:98524325-98526327	A549	lung:	n/a	n/a
8	RUNX3	chr3:98525274-98525859	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU6-26P	TF binding region
DCBLD2	TF binding region

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	1.00[AMR][1000 genomes]
rs1383908	1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	1.00[AMR][1000 genomes]
rs1600788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	1.00[YRI][hapmap]
rs1822019	1.00[AMR][1000 genomes]
rs1972432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2173598	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439232	0.84[YRI][hapmap]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.85[YRI][hapmap]
rs2470828	1.00[AMR][1000 genomes]
rs2470839	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	1.00[AMR][1000 genomes]
rs2470856	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278375	0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929491	0.85[YRI][hapmap]
rs4273318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	1.00[AMR][1000 genomes]
rs5013928	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs7373983	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626395	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828611	0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs828619	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs965757	1.00[AMR][1000 genomes]
rs974981	1.00[AMR][1000 genomes]
rs9883226	1.00[YRI][hapmap]
rs996199	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98503400-98576400	Weak transcription	Gastric	stomach
3	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
4	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
8	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
10	chr3:98516800-98528600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
12	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
13	chr3:98520200-98525600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:98520600-98528200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr3:98523400-98531400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:98523600-98525600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:98523600-98526200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:98523600-98526600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:98523600-98527000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:98523600-98527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:98523600-98527000	Strong transcription	Adipose Nuclei	Adipose
23	chr3:98523600-98527200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:98523600-98527400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:98523600-98528200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:98523600-98528600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:98523800-98525600	Strong transcription	HMEC	breast
30	chr3:98523800-98526000	Strong transcription	NHEK	skin
31	chr3:98523800-98526400	Strong transcription	Aorta	Aorta
32	chr3:98523800-98526400	Strong transcription	Brain Angular Gyrus	brain
33	chr3:98523800-98526400	Strong transcription	Fetal Stomach	stomach
34	chr3:98523800-98526400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:98523800-98526600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:98523800-98526600	Strong transcription	Brain Cingulate Gyrus	brain
37	chr3:98523800-98526600	Strong transcription	Colon Smooth Muscle	Colon
38	chr3:98523800-98526600	Strong transcription	Fetal Thymus	thymus
39	chr3:98523800-98526600	Strong transcription	HSMMtube	muscle
40	chr3:98523800-98526800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:98523800-98526800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:98523800-98526800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:98523800-98526800	Strong transcription	A549	lung
44	chr3:98523800-98527000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:98523800-98527000	Strong transcription	Liver	Liver
46	chr3:98523800-98527000	Strong transcription	Pancreas	Pancrea
47	chr3:98523800-98527000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:98523800-98527000	Strong transcription	K562	blood
49	chr3:98523800-98527200	Strong transcription	Brain Germinal Matrix	brain
50	chr3:98523800-98527200	Strong transcription	Ovary	ovary

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