Variant report

Variant	rs55978957
Chromosome Location	chr4:87569574-87569575
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10008165	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10023787	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10030525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031843	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1021101	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026861	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10516778	0.81[ASN][1000 genomes]
rs11097115	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943428	0.89[ASN][1000 genomes]
rs11947018	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1481833	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17011986	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17419295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17419627	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17419929	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17420607	0.81[ASN][1000 genomes]
rs17453839	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17454154	0.81[ASN][1000 genomes]
rs28483710	0.89[ASN][1000 genomes]
rs28485273	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28529445	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28534599	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28535527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663376	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28678816	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28735881	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4277747	0.84[ASN][1000 genomes]
rs4513526	0.89[ASN][1000 genomes]
rs55640323	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55654230	0.86[ASN][1000 genomes]
rs55746316	0.89[ASN][1000 genomes]
rs55757426	0.89[ASN][1000 genomes]
rs55773619	0.89[ASN][1000 genomes]
rs55879246	0.89[ASN][1000 genomes]
rs56150118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56178389	0.87[ASN][1000 genomes]
rs56296936	0.89[ASN][1000 genomes]
rs56348925	0.87[ASN][1000 genomes]
rs6531932	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66669421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67274037	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67341369	0.84[ASN][1000 genomes]
rs67523832	0.86[ASN][1000 genomes]
rs67928053	0.89[ASN][1000 genomes]
rs72665759	0.87[ASN][1000 genomes]
rs72665762	0.87[ASN][1000 genomes]
rs72665769	0.86[ASN][1000 genomes]
rs72665771	0.89[ASN][1000 genomes]
rs72665772	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72665777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7694723	0.85[ASN][1000 genomes]
rs9307020	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs969734	0.81[ASN][1000 genomes]
rs9993042	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87544400-87571200	Weak transcription	Pancreas	Pancrea
3	chr4:87556200-87570800	Weak transcription	Fetal Stomach	stomach
4	chr4:87557600-87569600	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:87557600-87571000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:87557600-87571200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:87557800-87569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:87557800-87569600	Weak transcription	Fetal Lung	lung
9	chr4:87557800-87570200	Weak transcription	Ovary	ovary
10	chr4:87561000-87570000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:87561800-87569600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:87563000-87571000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:87563800-87569800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87564400-87570800	Weak transcription	Fetal Intestine Small	intestine
15	chr4:87566400-87571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:87566400-87578400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:87566600-87570800	Weak transcription	NHEK	skin
18	chr4:87566600-87571200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:87566600-87578600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:87566800-87569600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:87567000-87571400	Weak transcription	NHDF-Ad	bronchial
22	chr4:87567800-87570200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:87567800-87571200	Weak transcription	Esophagus	oesophagus
24	chr4:87568600-87571400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:87568800-87569800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr4:87568800-87571800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:87568800-87573400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:87568800-87575200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:87569400-87570000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:87569400-87570200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:87569400-87571400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:87569400-87571800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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