Variant report

Variant	rs71516924
Chromosome Location	chr1:180961121-180961122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180960469..180962461-chr1:180967294..180968970,2	K562	blood:
2	chr1:180942605..180944590-chr1:180960185..180961783,2	K562	blood:
3	chr1:180954145..180958035-chr1:180958971..180961801,3	MCF-7	breast:
4	chr1:180960626..180962890-chr1:180962900..180965318,3	MCF-7	breast:
5	chr1:180960232..180962102-chr1:180991269..180993871,3	MCF-7	breast:
6	chr1:180958996..180961747-chr1:180978821..180982179,3	K562	blood:

Variant related genes	Relation type
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10494536	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10797662	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10797663	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3789361	0.82[EUR][1000 genomes]
rs3827708	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6425659	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7528255	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546157	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556005	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883859	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
5	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:180944400-180962600	Strong transcription	Osteobl	bone
7	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:180948600-180961400	Strong transcription	Fetal Intestine Large	intestine
11	chr1:180949000-180962400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:180949000-180962600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:180949400-180963800	Strong transcription	Liver	Liver
14	chr1:180949800-180962600	Strong transcription	Adipose Nuclei	Adipose
15	chr1:180949800-180962600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:180949800-180963800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:180949800-180966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:180950000-180962600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:180950000-180964600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:180950000-180965200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:180950000-180966400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:180950000-180968200	Strong transcription	HMEC	breast
23	chr1:180950600-180962400	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr1:180950800-180962400	Strong transcription	Placenta	Placenta
25	chr1:180951400-180966200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:180951600-180963800	Strong transcription	Fetal Lung	lung
27	chr1:180951600-180964800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:180951600-180966400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:180951800-180963600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:180952000-180963000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:180952000-180963200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:180952000-180963800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:180952000-180965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:180952000-180966000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:180952000-180966200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:180952200-180961200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:180952200-180962200	Strong transcription	GM12878-XiMat	blood
38	chr1:180952200-180964000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:180952200-180974800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:180952400-180963800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:180952600-180966000	Strong transcription	Fetal Thymus	thymus
42	chr1:180952800-180966000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:180953000-180962400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:180953200-180961600	Strong transcription	Thymus	Thymus
45	chr1:180953200-180962400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:180953200-180963000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:180953200-180963800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:180953400-180961200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:180953400-180961400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:180953400-180962200	Strong transcription	Primary B cells from peripheral blood	blood

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