Variant report

Variant	rs55954200
Chromosome Location	chr3:195842851-195842852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195806478..195810284-chr3:195841683..195844723,4	K562	blood:
2	chr3:195840171..195844762-chr3:195850259..195853821,6	K562	blood:
3	chr3:195840247..195843702-chr3:195870905..195872821,3	K562	blood:
4	chr3:195806881..195810211-chr3:195840128..195843050,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072274	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11920260	1.00[EUR][1000 genomes]
rs17091378	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56111861	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56964768	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57230784	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57512444	1.00[EUR][1000 genomes]
rs59223325	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59644311	0.83[AMR][1000 genomes]
rs59696970	0.83[AMR][1000 genomes]
rs59899056	1.00[EUR][1000 genomes]
rs59933501	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60102565	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61148961	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61504258	1.00[EUR][1000 genomes]
rs6765232	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73076359	1.00[EUR][1000 genomes]
rs73079255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73891194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7623992	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv1010395	chr3:195641908-195848264	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS 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	56 gene(s)	inside rSNPs	diseases
4	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv878170	chr3:195677895-195871388	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1002584	chr3:195734933-195910772	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
11	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv1002065	chr3:195769609-195877692	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv461130	chr3:195776240-195907653	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
15	nsv593069	chr3:195776240-195907653	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
16	nsv1005558	chr3:195789462-195919077	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
17	nsv536890	chr3:195789462-195919077	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
18	nsv998042	chr3:195840858-195934070	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195835600-195847000	Weak transcription	Esophagus	oesophagus
2	chr3:195835600-195847000	Weak transcription	Right Atrium	heart
3	chr3:195835600-195850000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:195835800-195853800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:195837800-195846000	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:195838000-195848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:195839000-195847000	Weak transcription	K562	blood
8	chr3:195839600-195843200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:195839600-195847000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:195839800-195847200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:195840000-195844000	Weak transcription	Fetal Thymus	thymus
12	chr3:195840200-195845800	Enhancers	Primary B cells from cord blood	blood
13	chr3:195841000-195845000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:195841600-195844800	Weak transcription	Placenta	Placenta
15	chr3:195841600-195845400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:195841600-195847200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:195842400-195843000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:195842400-195843000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:195842400-195843600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:195842400-195845800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:195842400-195847400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:195842600-195843000	Active TSS	GM12878-XiMat	blood
23	chr3:195842600-195843400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr3:195842600-195843400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:195842600-195851200	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:195842800-195843000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:195842800-195843400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:195842800-195843600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:195842800-195844000	Enhancers	Primary T cells from cord blood	blood
30	chr3:195842800-195844000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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