Variant report

Variant	rs1972432
Chromosome Location	chr3:98605720-98605721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98603937..98606892-chr3:98607336..98610177,2	MCF-7	breast:
2	chr3:98605105..98607853-chr3:98609864..98612381,4	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036674	1.00[AMR][1000 genomes]
rs10935512	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1095913	1.00[AMR][1000 genomes]
rs1095914	1.00[AMR][1000 genomes]
rs1351496	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383908	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1383911	1.00[AMR][1000 genomes]
rs1440157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1600788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1818053	0.83[AFR][1000 genomes]
rs1822019	1.00[AMR][1000 genomes]
rs2099738	1.00[AMR][1000 genomes]
rs2119189	1.00[AMR][1000 genomes]
rs2128053	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2133575	0.95[AFR][1000 genomes]
rs2173598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439227	1.00[AMR][1000 genomes]
rs2439230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439233	1.00[AMR][1000 genomes]
rs2439234	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2439235	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2448985	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454675	1.00[AMR][1000 genomes]
rs2454681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470820	0.84[AFR][1000 genomes]
rs2470828	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470850	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2470856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470866	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470874	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2470884	0.95[AFR][1000 genomes]
rs278375	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278378	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278384	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278385	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278386	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278389	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2922213	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2929491	0.84[AFR][1000 genomes]
rs4273318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4857107	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5013928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440189	0.84[AFR][1000 genomes]
rs6440232	1.00[AMR][1000 genomes]
rs6795351	0.92[AFR][1000 genomes]
rs7373983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73858658	0.81[AFR][1000 genomes]
rs7626395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630797	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828604	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828607	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828619	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828620	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828622	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828623	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828624	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs866873	0.82[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]
rs974982	0.81[AFR][1000 genomes]
rs996199	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
6	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
7	chr3:98595200-98608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:98596200-98606600	Weak transcription	HepG2	liver
9	chr3:98597000-98609000	Weak transcription	Right Ventricle	heart
10	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:98598200-98608400	Weak transcription	Fetal Intestine Small	intestine
12	chr3:98599200-98609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:98599800-98609000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
15	chr3:98600000-98609600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:98600600-98607200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:98600600-98611200	Weak transcription	Liver	Liver
18	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
21	chr3:98602200-98608600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
23	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:98603200-98612600	Genic enhancers	NHEK	skin
25	chr3:98603400-98606400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:98603400-98606400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:98603400-98607600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:98603600-98606200	Enhancers	Adipose Nuclei	Adipose
29	chr3:98603600-98608000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:98603800-98607200	Weak transcription	Brain Substantia Nigra	brain
31	chr3:98603800-98608000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr3:98604000-98606000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:98604000-98606200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:98604000-98608400	Enhancers	HUVEC	blood vessel
35	chr3:98604000-98613000	Enhancers	NHLF	lung
36	chr3:98604200-98606200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:98604200-98606200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:98604200-98606200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:98604200-98606400	Enhancers	Fetal Kidney	kidney
40	chr3:98604200-98608000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:98604200-98612600	Enhancers	NHDF-Ad	bronchial
42	chr3:98604400-98606200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:98604400-98608800	Enhancers	Fetal Heart	heart
44	chr3:98604400-98610400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:98604400-98611400	Genic enhancers	HMEC	breast
46	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:98604600-98609000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:98604800-98606600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:98604800-98606600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:98604800-98606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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