Variant report

Variant	rs56073423
Chromosome Location	chr3:133930090-133930091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:133929883-133931301	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:133916227..133917047-chr3:133930033..133930914,2	K562	blood:
2	chr3:133929438..133933511-chr3:133934266..133936727,4	K562	blood:
3	chr3:133915566..133917732-chr3:133929901..133931438,2	MCF-7	breast:
4	chr3:133929711..133931992-chr3:134027528..134029983,2	MCF-7	breast:
5	chr3:133927446..133930407-chr3:133968665..133970710,2	MCF-7	breast:

No data

Variant related genes	Relation type
RYK	TF binding region
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10935104	0.82[EUR][1000 genomes]
rs1131262	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707763	0.88[ASN][1000 genomes]
rs11915143	0.88[ASN][1000 genomes]
rs35322473	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3890774	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072180	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324466	0.89[ASN][1000 genomes]
rs4682664	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682666	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682668	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682669	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55689708	0.81[ASN][1000 genomes]
rs6439465	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439466	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650893	0.88[ASN][1000 genomes]
rs6762690	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776502	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780295	0.88[ASN][1000 genomes]
rs6800143	0.89[ASN][1000 genomes]
rs6808085	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355922	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7609611	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622046	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283588	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812461	0.85[ASN][1000 genomes]
rs9818714	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823873	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825808	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827728	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9832732	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839819	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853568	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856298	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856792	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858069	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858450	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9858707	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 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	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
2	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
3	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
4	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
6	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:133895000-133950200	Weak transcription	Gastric	stomach
8	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:133902000-133930400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:133918000-133930200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:133918000-133930400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:133918400-133930400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:133919000-133950600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:133919400-133943000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:133919600-133930800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:133919800-133940200	Weak transcription	Esophagus	oesophagus
18	chr3:133920000-133940200	Weak transcription	Fetal Intestine Small	intestine
19	chr3:133920200-133934000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:133920200-133938200	Weak transcription	Fetal Brain Male	brain
21	chr3:133920400-133938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:133920600-133932000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:133920600-133938400	Weak transcription	HSMMtube	muscle
24	chr3:133920600-133940600	Weak transcription	A549	lung
25	chr3:133920800-133931800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:133920800-133932000	Weak transcription	Ovary	ovary
27	chr3:133920800-133940600	Weak transcription	Thymus	Thymus
28	chr3:133920800-133950200	Weak transcription	Aorta	Aorta
29	chr3:133920800-133950200	Weak transcription	Spleen	Spleen
30	chr3:133920800-133950600	Weak transcription	Hela-S3	cervix
31	chr3:133921200-133930600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:133921200-133931800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:133921400-133934600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:133921600-133932000	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:133921600-133937200	Weak transcription	Fetal Stomach	stomach
36	chr3:133921600-133941800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:133921800-133931800	Weak transcription	Brain Angular Gyrus	brain
38	chr3:133921800-133943000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:133923000-133930800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:133923600-133930400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:133923600-133931200	Strong transcription	Primary T cells from cord blood	blood
42	chr3:133923800-133934200	Strong transcription	Primary B cells from cord blood	blood
43	chr3:133924200-133930200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:133924200-133930400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:133924600-133941800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:133925200-133930200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:133925400-133930200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr3:133925400-133930400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:133925400-133930400	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:133925400-133930600	Strong transcription	Primary hematopoietic stem cells	blood

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