Variant report

Variant	rs72961930
Chromosome Location	chr3:51963977-51963978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51963363..51966858-chr3:51969595..51972512,3	MCF-7	breast:
2	chr3:51962409..51965326-chr3:51965787..51967920,2	K562	blood:
3	chr3:51963488..51965145-chr3:51974504..51977314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	1.00[AMR][1000 genomes]
rs323869	1.00[AMR][1000 genomes]
rs323870	1.00[AMR][1000 genomes]
rs323872	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323880	1.00[AMR][1000 genomes]
rs323889	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	1.00[AMR][1000 genomes]
rs323896	1.00[AMR][1000 genomes]
rs323900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368210	1.00[AMR][1000 genomes]
rs422304	1.00[AMR][1000 genomes]
rs56746340	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964016	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7426999	1.00[AMR][1000 genomes]
rs7636204	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51950600-51967000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51956800-51964400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:51960400-51964800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:51960600-51974400	Weak transcription	Fetal Brain Male	brain
5	chr3:51961400-51965000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:51961400-51966400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:51961400-51966600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:51961800-51964400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:51962000-51966800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:51962200-51965000	Weak transcription	Liver	Liver
11	chr3:51962200-51966000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:51962200-51966600	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:51962400-51964000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:51962600-51965000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:51962600-51965800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:51962600-51966600	Weak transcription	Spleen	Spleen
17	chr3:51962600-51966800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:51962600-51973200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:51962800-51964400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:51962800-51964400	Weak transcription	Thymus	Thymus
21	chr3:51962800-51965000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:51962800-51965000	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:51962800-51965600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:51962800-51966000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:51962800-51966600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:51962800-51966600	Weak transcription	Gastric	stomach
27	chr3:51962800-51966800	Weak transcription	NHLF	lung
28	chr3:51963000-51964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:51963000-51964600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:51963000-51965000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:51963000-51966000	Weak transcription	Osteobl	bone
32	chr3:51963000-51966400	Weak transcription	Brain Anterior Caudate	brain
33	chr3:51963200-51965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:51963200-51965000	Weak transcription	Fetal Stomach	stomach
35	chr3:51963200-51965400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:51963400-51965000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:51963400-51965000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:51963400-51965000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:51963400-51965000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:51963400-51965000	Weak transcription	Lung	lung
41	chr3:51963400-51965200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:51963400-51965200	Weak transcription	NH-A	brain
43	chr3:51963400-51965600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:51963400-51966600	Weak transcription	Fetal Brain Female	brain
45	chr3:51963400-51966800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:51963600-51965200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:51963600-51965200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:51963600-51965200	Weak transcription	Fetal Intestine Small	intestine
49	chr3:51963600-51965800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:51963600-51965800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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