Variant report

Variant	rs3930
Chromosome Location	chr2:53897525-53897526
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53887538..53889702-chr2:53894811..53897627,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10490465	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11900355	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13428687	0.88[ASN][1000 genomes]
rs13428898	0.91[ASN][1000 genomes]
rs17039525	0.82[ASN][1000 genomes]
rs17045037	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17045048	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17045065	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17045081	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17045084	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34408637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35487539	0.81[ASN][1000 genomes]
rs3731970	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770408	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770409	0.94[ASN][1000 genomes]
rs3770411	0.89[CEU][hapmap]
rs4525731	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55861447	0.91[ASN][1000 genomes]
rs56081218	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56311225	0.89[ASN][1000 genomes]
rs56383522	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58125503	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58359565	0.81[ASN][1000 genomes]
rs58515086	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60282090	0.96[ASN][1000 genomes]
rs61671599	0.86[ASN][1000 genomes]
rs62139773	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62139774	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62139775	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62139785	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62139788	0.96[ASN][1000 genomes]
rs62139836	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72901209	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73934971	0.89[ASN][1000 genomes]
rs7583622	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs7600981	0.96[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	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53883200-53897800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
5	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
6	chr2:53887000-53898000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:53887800-53899800	Weak transcription	Primary B cells from cord blood	blood
8	chr2:53888200-53934200	Weak transcription	Lung	lung
9	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
10	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
11	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:53891600-53900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:53892600-53902600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
15	chr2:53893400-53915200	Weak transcription	Ovary	ovary
16	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:53894400-53900400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:53894400-53912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:53894600-53900000	Weak transcription	Stomach Mucosa	stomach
24	chr2:53894600-53911200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:53894800-53900000	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:53895000-53900200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:53895000-53911800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:53895200-53898000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:53895400-53898600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
31	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:53895800-53897600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:53895800-53897600	Strong transcription	Dnd41	blood
38	chr2:53895800-53897800	Strong transcription	Fetal Thymus	thymus
39	chr2:53895800-53916800	Weak transcription	Brain Anterior Caudate	brain
40	chr2:53895800-53926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:53896000-53897600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:53896000-53898200	Strong transcription	Primary T cells from cord blood	blood
43	chr2:53896000-53899400	Weak transcription	GM12878-XiMat	blood
44	chr2:53896000-53900000	Weak transcription	HSMM	muscle
45	chr2:53896000-53913000	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:53896000-53918800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:53896200-53897800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:53896200-53911200	Weak transcription	Liver	Liver
49	chr2:53896200-53918400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:53896400-53897600	Weak transcription	NHDF-Ad	bronchial

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