Variant report

Variant	rs9843299
Chromosome Location	chr3:52137469-52137470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52131304..52133205-chr3:52136304..52138241,3	K562	blood:
2	chr3:52135638..52138438-chr3:52142187..52143836,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12386365	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314125	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13319566	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164638	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164639	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17051957	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17051977	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171294	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183029	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304505	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28452586	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28659792	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352146	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352147	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352148	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352149	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352150	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352151	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352153	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55664415	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55834589	0.91[EUR][1000 genomes]
rs56281986	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322622	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57335685	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57466127	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59890038	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781635	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72964042	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72964044	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638246	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808787	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876782	0.94[EUR][1000 genomes]
rs893056	0.97[EUR][1000 genomes]
rs9809254	0.91[EUR][1000 genomes]
rs9809977	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811707	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815010	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816434	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9817653	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830293	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841469	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843852	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846049	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847073	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847092	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857878	0.97[EUR][1000 genomes]
rs9860982	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9868101	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882775	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
8	nsv963259	chr3:52131542-52139351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
3	chr3:52122000-52140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:52122800-52142200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:52124200-52138200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:52124200-52157200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52124800-52142000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:52125000-52140400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:52125400-52138400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:52125800-52139800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:52125800-52142400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:52126200-52160600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:52127400-52139200	Weak transcription	Esophagus	oesophagus
14	chr3:52128200-52140800	Weak transcription	Spleen	Spleen
15	chr3:52128400-52142200	Weak transcription	NHDF-Ad	bronchial
16	chr3:52128400-52142600	Weak transcription	NH-A	brain
17	chr3:52128600-52157000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:52129200-52155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:52131400-52138600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52131600-52142800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:52132000-52138400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:52132000-52140600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:52132200-52146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:52132200-52155200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52132400-52142600	Weak transcription	NHLF	lung
26	chr3:52132400-52143600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:52132600-52140600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:52133000-52142400	Weak transcription	Fetal Lung	lung
29	chr3:52133000-52142400	Weak transcription	K562	blood
30	chr3:52133200-52140600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:52133200-52141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:52133200-52142600	Weak transcription	Lung	lung
33	chr3:52133200-52143600	Weak transcription	HUVEC	blood vessel
34	chr3:52133200-52162000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:52133400-52138600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:52133400-52138800	Weak transcription	Left Ventricle	heart
37	chr3:52133400-52138800	Weak transcription	Thymus	Thymus
38	chr3:52133400-52139400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:52133400-52140400	Weak transcription	HMEC	breast
40	chr3:52133400-52142800	Weak transcription	Pancreas	Pancrea
41	chr3:52133400-52143800	Weak transcription	Stomach Mucosa	stomach
42	chr3:52133400-52144600	Weak transcription	Gastric	stomach
43	chr3:52133400-52155000	Weak transcription	Osteobl	bone
44	chr3:52133600-52137800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:52133600-52142400	Weak transcription	HepG2	liver
46	chr3:52134600-52140400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:52135400-52138600	Weak transcription	Fetal Intestine Small	intestine
48	chr3:52135400-52140600	Weak transcription	Fetal Stomach	stomach
49	chr3:52135400-52140600	Weak transcription	Fetal Thymus	thymus
50	chr3:52135400-52142000	Weak transcription	Primary monocytes fromperipheralblood	blood

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