Variant report

Variant	rs72941434
Chromosome Location	chr3:100057109-100057110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100056720-100057772	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:100057025-100057182	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10511179	0.82[ASN][1000 genomes]
rs11918399	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11919543	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919627	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16842142	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772687	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55699261	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55864663	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56012915	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56956506	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57155242	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57166766	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57332305	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57703319	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59304656	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59396265	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59491720	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59507591	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59509062	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60463428	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60999188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941452	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941453	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941454	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941473	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941482	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv3387925	chr3:100056362-100059860	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3392416	chr3:100056925-100057181	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:100054600-100057200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
8	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
9	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
14	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
20	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:100054800-100057200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:100054800-100057200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:100054800-100057200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:100054800-100057200	Weak transcription	Primary B cells from cord blood	blood
25	chr3:100054800-100057200	Weak transcription	HSMM	muscle
26	chr3:100054800-100057200	Weak transcription	Osteobl	bone
27	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:100054800-100057800	Enhancers	Liver	Liver
35	chr3:100054800-100057800	Weak transcription	Gastric	stomach
36	chr3:100054800-100057800	Weak transcription	Ovary	ovary
37	chr3:100054800-100057800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:100054800-100057800	Weak transcription	NHDF-Ad	bronchial
39	chr3:100054800-100058000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:100054800-100058000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:100054800-100058000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:100054800-100058000	Weak transcription	Fetal Thymus	thymus
43	chr3:100054800-100058000	Weak transcription	Left Ventricle	heart
44	chr3:100054800-100058000	Weak transcription	Lung	lung
45	chr3:100054800-100058000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:100054800-100058000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:100054800-100058000	Weak transcription	HSMMtube	muscle
48	chr3:100054800-100058400	Weak transcription	NH-A	brain
49	chr3:100054800-100058600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:100054800-100058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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