Variant report

Variant	rs3204850
Chromosome Location	chr3:46450297-46450298
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	chr3:46448132-46450759	PBDE	blood:	n/a	n/a
2	RAD21	chr3:46450294-46450748	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000223552	TF binding region
CCRL2	TF binding region

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs11574430	1.00[ASN][1000 genomes]
rs11574436	1.00[ASN][1000 genomes]
rs11574442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575062	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13065351	1.00[AFR][1000 genomes]
rs13071469	1.00[AFR][1000 genomes]
rs13073976	1.00[AFR][1000 genomes]
rs13077302	1.00[AFR][1000 genomes]
rs13078564	1.00[AFR][1000 genomes]
rs13080757	1.00[AFR][1000 genomes]
rs13093063	1.00[AFR][1000 genomes]
rs17141079	0.90[ASN][1000 genomes]
rs17141101	1.00[ASN][1000 genomes]
rs17283712	1.00[AFR][1000 genomes]
rs17284138	1.00[AFR][1000 genomes]
rs17284187	1.00[AFR][1000 genomes]
rs17285143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17715106	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17765882	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17782551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782618	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782636	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894387	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1894388	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2097285	0.93[EUR][1000 genomes]
rs2157052	0.83[EUR][1000 genomes]
rs2157053	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2157055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2856762	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3091310	1.00[AFR][1000 genomes]
rs3092957	0.90[ASN][1000 genomes]
rs3092958	0.90[ASN][1000 genomes]
rs3092959	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3181038	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34024447	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34041956	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34073838	1.00[AFR][1000 genomes]
rs34079287	1.00[AFR][1000 genomes]
rs34106161	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34158148	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34180919	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34190223	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34200951	0.95[ASN][1000 genomes]
rs34203322	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34245951	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34265215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34351442	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34363105	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34448949	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34455547	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34473395	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34578126	0.86[ASN][1000 genomes]
rs34671664	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34709208	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34883716	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34953706	0.90[ASN][1000 genomes]
rs34988015	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34997818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35117954	1.00[AFR][1000 genomes]
rs35118578	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35148665	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35218998	1.00[AFR][1000 genomes]
rs35260614	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35367413	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35373513	1.00[AFR][1000 genomes]
rs35386789	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35413141	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35438577	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35479331	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35511592	1.00[AFR][1000 genomes]
rs35513549	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35516519	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35568430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35577626	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35601704	0.90[ASN][1000 genomes]
rs35646896	1.00[AFR][1000 genomes]
rs35821444	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35878193	0.95[ASN][1000 genomes]
rs35883833	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35943069	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs36020695	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36030692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36052732	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs36078103	1.00[AFR][1000 genomes]
rs3749461	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3918354	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3918362	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3918365	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4473594	1.00[AFR][1000 genomes]
rs6777875	0.90[ASN][1000 genomes]
rs6806951	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71327048	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs71327052	0.90[ASN][1000 genomes]
rs71327053	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71327054	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71327055	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71327056	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71327057	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs71327059	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71327061	0.90[ASN][1000 genomes]
rs71327062	0.95[ASN][1000 genomes]
rs71327063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71327065	0.86[ASN][1000 genomes]
rs71615445	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9714000	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46446800-46450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:46448200-46452000	Enhancers	Dnd41	blood
4	chr3:46448400-46450400	Enhancers	Fetal Heart	heart
5	chr3:46448600-46460000	Weak transcription	Gastric	stomach
6	chr3:46448800-46450400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:46449200-46450400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:46449200-46451400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:46449200-46451800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:46449400-46450400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:46449400-46450400	Enhancers	Fetal Muscle Leg	muscle
12	chr3:46449400-46450600	Enhancers	Left Ventricle	heart
13	chr3:46449400-46450600	Enhancers	NH-A	brain
14	chr3:46449400-46450800	Enhancers	Psoas Muscle	Psoas
15	chr3:46449400-46453000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:46449600-46450400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:46449600-46450800	Genic enhancers	Primary T cells from cord blood	blood
18	chr3:46449600-46451000	Genic enhancers	Fetal Intestine Small	intestine
19	chr3:46449600-46451200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:46449600-46451200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:46449600-46452000	Enhancers	K562	blood
22	chr3:46449600-46453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:46449600-46454000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:46449600-46457600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:46449800-46450400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:46449800-46450400	Genic enhancers	Thymus	Thymus
27	chr3:46449800-46451000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:46449800-46451000	Genic enhancers	Fetal Thymus	thymus
29	chr3:46449800-46451200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:46449800-46451400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:46449800-46451800	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:46449800-46452000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:46449800-46453800	Weak transcription	Small Intestine	intestine
34	chr3:46450000-46450400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:46450000-46450600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:46450000-46450600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:46450000-46450600	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr3:46450000-46450600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:46450000-46451200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr3:46450000-46451200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:46450000-46451600	Weak transcription	Brain Anterior Caudate	brain
42	chr3:46450000-46451600	Weak transcription	Spleen	Spleen
43	chr3:46450000-46457600	Weak transcription	Stomach Mucosa	stomach
44	chr3:46450000-46457800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:46450200-46450400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:46450200-46450600	Enhancers	HSMM	muscle
47	chr3:46450200-46450600	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:46450200-46450600	Enhancers	Osteobl	bone
49	chr3:46450200-46450800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:46450200-46450800	Enhancers	HUVEC	blood vessel

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