Variant report

Variant	rs28553548
Chromosome Location	chr3:81807348-81807349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:81806041..81808024-chr3:81808030..81809607,2	K562	blood:
2	chr3:81804346..81807899-chr3:81808631..81812323,5	MCF-7	breast:
3	chr3:81803251..81808051-chr3:81808352..81812027,5	K562	blood:

Variant related genes	Relation type
ENSG00000114480	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13314900	0.91[EUR][1000 genomes]
rs1404296	0.82[EUR][1000 genomes]
rs1851922	0.87[EUR][1000 genomes]
rs1973802	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2680275	0.85[EUR][1000 genomes]
rs2680276	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28630448	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28637864	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3772886	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57555994	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59419728	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62265681	0.80[EUR][1000 genomes]
rs62267115	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62267150	0.90[EUR][1000 genomes]
rs6548778	0.80[EUR][1000 genomes]
rs6768673	0.87[EUR][1000 genomes]
rs6776410	0.86[EUR][1000 genomes]
rs6785740	0.84[EUR][1000 genomes]
rs6791629	0.88[EUR][1000 genomes]
rs6798822	0.85[EUR][1000 genomes]
rs6804613	0.85[EUR][1000 genomes]
rs6804697	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633528	0.80[EUR][1000 genomes]
rs7634830	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813371	0.90[EUR][1000 genomes]
rs9816203	0.80[EUR][1000 genomes]
rs9816946	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820490	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821222	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9825400	0.85[EUR][1000 genomes]
rs9831301	0.90[EUR][1000 genomes]
rs9831360	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9833851	0.82[EUR][1000 genomes]
rs9838598	0.85[EUR][1000 genomes]
rs9851559	0.90[EUR][1000 genomes]
rs9863322	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870979	0.85[EUR][1000 genomes]
rs9874754	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:81791200-81808800	Weak transcription	Primary T cells from cord blood	blood
4	chr3:81792000-81810200	Weak transcription	Spleen	Spleen
5	chr3:81793000-81809600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:81793200-81809200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:81793800-81808600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:81793800-81809200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:81793800-81810000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:81794400-81808600	Weak transcription	K562	blood
11	chr3:81795600-81810000	Weak transcription	Lung	lung
12	chr3:81796000-81808600	Weak transcription	Small Intestine	intestine
13	chr3:81796200-81809200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:81796800-81809200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:81797400-81809800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:81798400-81809000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:81799000-81808600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:81799400-81808400	Weak transcription	Hela-S3	cervix
19	chr3:81799400-81808600	Weak transcription	Fetal Heart	heart
20	chr3:81799400-81809400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:81799800-81809800	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:81800400-81809400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:81800400-81809400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:81800800-81809400	Weak transcription	Brain Substantia Nigra	brain
25	chr3:81801800-81809200	Weak transcription	Fetal Intestine Small	intestine
26	chr3:81802000-81807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:81802200-81808600	Weak transcription	Fetal Kidney	kidney
28	chr3:81802800-81809000	ZNF genes & repeats	GM12878-XiMat	blood
29	chr3:81803000-81808600	Weak transcription	Pancreas	Pancrea
30	chr3:81803400-81809800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:81804200-81809200	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:81804200-81809800	Weak transcription	Esophagus	oesophagus
33	chr3:81804600-81808000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:81804600-81808600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:81804600-81808800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:81804600-81808800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:81805000-81809400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:81805400-81807400	Strong transcription	Primary B cells from cord blood	blood
39	chr3:81805400-81808800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:81805600-81808800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:81805600-81811600	Active TSS	Right Ventricle	heart
42	chr3:81805800-81808000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:81805800-81809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:81806000-81807800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:81806400-81807600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:81806400-81807600	Genic enhancers	Liver	Liver
47	chr3:81806400-81808800	ZNF genes & repeats	A549	lung
48	chr3:81806400-81810000	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr3:81806600-81807400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:81806600-81807400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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