Variant report

Variant	rs2548411
Chromosome Location	chr5:96516396-96516397
allele	C/T
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	chr5:96516204-96516565	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96268592..96270496-chr5:96515475..96517242,2	MCF-7	breast:
2	chr5:96508014..96513294-chr5:96513654..96520413,9	K562	blood:
3	chr5:96513279..96516622-chr5:96517923..96519975,3	MCF-7	breast:
4	chr5:96142348..96145031-chr5:96516210..96518138,3	K562	blood:

Variant related genes	Relation type
ENSG00000251513	TF binding region
RNU1-73P	TF binding region
ENSG00000164307	Chromatin interaction
ENSG00000058729	Chromatin interaction
ENSG00000206698	Chromatin interaction
ENSG00000251513	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1645200	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2432091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2432123	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2544770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30998	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30999	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs31001	0.88[ASN][1000 genomes]
rs31007	0.93[EUR][1000 genomes]
rs31008	0.85[EUR][1000 genomes]
rs3806945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806946	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs731021	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882391	chr5:96496189-96533469	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
8	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv3348846	chr5:96514946-96516894	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96494400-96518000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:96494600-96516600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:96494800-96516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:96494800-96516400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr5:96494800-96516400	Strong transcription	Fetal Thymus	thymus
6	chr5:96494800-96516600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:96495200-96516800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:96495200-96518000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:96495400-96516600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:96495600-96517800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:96495800-96517400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:96496000-96516800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:96496600-96516400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:96497800-96516400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:96498000-96516400	Strong transcription	Placenta	Placenta
16	chr5:96503000-96516600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr5:96510200-96517200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:96512000-96516400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:96512200-96516400	Weak transcription	Fetal Intestine Small	intestine
20	chr5:96512400-96517200	Weak transcription	Fetal Stomach	stomach
21	chr5:96512600-96517000	Weak transcription	Small Intestine	intestine
22	chr5:96513600-96517400	Weak transcription	Brain Germinal Matrix	brain
23	chr5:96514600-96517200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:96514600-96517200	Weak transcription	Brain Substantia Nigra	brain
25	chr5:96514600-96517200	Weak transcription	Fetal Heart	heart
26	chr5:96514600-96517400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:96514600-96517400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:96514600-96517400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:96514600-96517400	Weak transcription	Fetal Brain Male	brain
30	chr5:96514600-96517400	Weak transcription	Gastric	stomach
31	chr5:96514600-96517400	Weak transcription	Pancreas	Pancrea
32	chr5:96514600-96517400	Weak transcription	Thymus	Thymus
33	chr5:96514600-96518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:96514600-96518000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:96514600-96518400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:96514600-96518600	Weak transcription	Spleen	Spleen
37	chr5:96514800-96517000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr5:96514800-96517200	Weak transcription	Aorta	Aorta
39	chr5:96514800-96517200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:96514800-96517200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:96514800-96517400	Weak transcription	Brain Angular Gyrus	brain
42	chr5:96514800-96517400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:96514800-96517400	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:96514800-96517400	Weak transcription	Right Ventricle	heart
45	chr5:96514800-96517600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:96514800-96517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:96514800-96517600	Weak transcription	Fetal Kidney	kidney
48	chr5:96514800-96518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:96514800-96518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:96514800-96518000	Weak transcription	Esophagus	oesophagus

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