Variant report

Variant	rs56402221
Chromosome Location	chr3:121148760-121148761
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11914436	0.95[EUR][1000 genomes]
rs3218634	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3898024	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4440066	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs482256	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs487848	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs494140	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501099	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs507353	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs532411	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs546930	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs552404	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs604231	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs630138	0.94[AFR][1000 genomes]
rs669277	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs697019	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs716688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73183172	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73191762	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs794323	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9289170	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9824168	0.91[EUR][1000 genomes]
rs9828736	0.91[EUR][1000 genomes]
rs9828910	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9860047	0.92[EUR][1000 genomes]
rs9868609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878946	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9883968	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv521397	chr3:120970900-121192350	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv829702	chr3:121045793-121227975	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv591398	chr3:121046468-121154193	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv591399	chr3:121046468-121160369	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv591401	chr3:121094592-121160369	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121129200-121148800	Weak transcription	GM12878-XiMat	blood
2	chr3:121134200-121152600	Weak transcription	Hela-S3	cervix
3	chr3:121135800-121149000	Weak transcription	A549	lung
4	chr3:121137800-121148800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:121139200-121150600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:121139200-121186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:121140200-121149000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:121140600-121150800	Weak transcription	HSMM	muscle
9	chr3:121140600-121170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:121140800-121149000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:121140800-121150800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:121140800-121151400	Weak transcription	HepG2	liver
13	chr3:121141000-121148800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:121141200-121186000	Weak transcription	NHEK	skin
15	chr3:121142200-121161600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:121142600-121151000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:121143200-121150800	Weak transcription	NHLF	lung
18	chr3:121143400-121150800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:121143600-121160000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:121144600-121150600	Strong transcription	Dnd41	blood
21	chr3:121144800-121150800	Weak transcription	HUVEC	blood vessel
22	chr3:121145200-121150600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:121145200-121160200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:121145400-121148800	Weak transcription	K562	blood
25	chr3:121145400-121150800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:121145400-121160600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:121145800-121149000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:121145800-121155800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:121145800-121161200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:121146000-121150600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:121146000-121177400	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:121146000-121185800	Weak transcription	Fetal Stomach	stomach
33	chr3:121146200-121149000	Weak transcription	HMEC	breast
34	chr3:121146200-121151000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:121146200-121154600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:121146200-121185600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:121146400-121152400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:121146400-121185800	Weak transcription	Fetal Intestine Large	intestine
39	chr3:121146800-121151800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:121147000-121148800	Weak transcription	Osteobl	bone
41	chr3:121147000-121153400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:121147000-121153800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:121147200-121150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:121147200-121153400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:121147400-121148800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:121147400-121148800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:121147400-121151000	Weak transcription	Brain Anterior Caudate	brain
48	chr3:121147800-121148800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:121147800-121149000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:121147800-121150600	Weak transcription	NHDF-Ad	bronchial

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