Variant report

Variant	rs2544773
Chromosome Location	chr5:96513471-96513472
allele	C/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	chr5:96513438-96513650	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96513470..96515096-chr5:96518937..96520609,2	MCF-7	breast:
2	chr5:96513279..96516622-chr5:96517923..96519975,3	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10072369	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12515176	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363943	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216709	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316183	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316184	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316185	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs316186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316193	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316196	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs316197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs316200	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316215	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35824066	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3906410	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs43497	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72777622	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96494400-96515200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:96494400-96518000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:96494600-96516600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:96494800-96514400	Weak transcription	Fetal Heart	heart
5	chr5:96494800-96515200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:96494800-96516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:96494800-96516400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr5:96494800-96516400	Strong transcription	Fetal Thymus	thymus
9	chr5:96494800-96516600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:96495000-96516000	Strong transcription	Dnd41	blood
11	chr5:96495000-96516200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:96495200-96515200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:96495200-96515400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr5:96495200-96516000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:96495200-96516800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:96495200-96518000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:96495400-96516600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:96495600-96515600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:96495600-96515800	Strong transcription	Osteobl	bone
20	chr5:96495600-96517800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:96495800-96517400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:96496000-96516800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:96496200-96515200	Strong transcription	NH-A	brain
24	chr5:96496400-96514000	Weak transcription	Aorta	Aorta
25	chr5:96496600-96514000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:96496600-96515600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:96496600-96516400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:96497800-96516400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:96498000-96516400	Strong transcription	Placenta	Placenta
30	chr5:96499000-96515000	Strong transcription	Adipose Nuclei	Adipose
31	chr5:96499400-96515200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:96499600-96514800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:96500000-96515400	Strong transcription	HMEC	breast
34	chr5:96500200-96514000	Weak transcription	Esophagus	oesophagus
35	chr5:96500400-96516000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:96501400-96515200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:96501600-96515000	Strong transcription	HUVEC	blood vessel
38	chr5:96501800-96515200	Strong transcription	Liver	Liver
39	chr5:96502000-96515200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:96502400-96515000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:96502400-96516000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:96502600-96514800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:96502600-96515400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:96502600-96516000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:96503000-96515400	Strong transcription	HSMM	muscle
46	chr5:96503000-96516600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr5:96503200-96515200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:96503200-96516000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:96503400-96514800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:96503600-96515200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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