Variant report

Variant	rs55944246
Chromosome Location	chr7:16458976-16458977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16441426..16443801-chr7:16458658..16460792,2	K562	blood:
2	chr7:16302626..16306339-chr7:16456665..16460333,5	K562	blood:
3	chr7:16456001..16461931-chr7:16682283..16687700,6	K562	blood:
4	chr7:16302978..16309646-chr7:16456908..16462647,13	K562	blood:
5	chr7:16455152..16459514-chr7:16459744..16463250,7	MCF-7	breast:
6	chr7:16456961..16459582-chr7:16459937..16461767,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229688	Chromatin interaction
ENSG00000106524	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000214960	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10464288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617508	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17674339	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1921840	0.84[ASN][1000 genomes]
rs1921843	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1921845	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389632	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389633	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2389638	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55746209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55790136	0.95[ASN][1000 genomes]
rs56061198	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56176134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56199980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59379368	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60255112	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461247	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67088819	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67609961	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73071078	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7791775	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758105	chr7:16272822-16527390	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1034151	chr7:16415497-16578081	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16434400-16459000	Weak transcription	Stomach Mucosa	stomach
2	chr7:16440400-16459600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:16450000-16459600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:16450600-16459800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:16453000-16459600	Weak transcription	Pancreas	Pancrea
6	chr7:16453000-16460400	Weak transcription	Gastric	stomach
7	chr7:16453800-16459400	Weak transcription	Fetal Heart	heart
8	chr7:16455400-16459600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:16455800-16459800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:16456400-16459600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:16456400-16459800	Weak transcription	Lung	lung
12	chr7:16456600-16459800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:16457200-16459600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:16457200-16459800	Weak transcription	NHLF	lung
15	chr7:16457400-16459600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:16457400-16459800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:16457400-16459800	Weak transcription	NH-A	brain
18	chr7:16457600-16459200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:16457800-16459400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:16457800-16459600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:16457800-16459600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:16457800-16459600	Weak transcription	Fetal Lung	lung
23	chr7:16457800-16459600	Weak transcription	HMEC	breast
24	chr7:16457800-16459600	Weak transcription	Osteobl	bone
25	chr7:16457800-16459800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:16457800-16459800	Weak transcription	HSMM	muscle
27	chr7:16457800-16459800	Weak transcription	HSMMtube	muscle
28	chr7:16457800-16459800	Weak transcription	NHDF-Ad	bronchial
29	chr7:16458000-16459600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:16458200-16459000	Flanking Active TSS	K562	blood
31	chr7:16458200-16459400	Weak transcription	Primary T cells from cord blood	blood
32	chr7:16458400-16459600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:16458600-16459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr7:16458600-16459800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:16458800-16459600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:16458800-16459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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