Variant report

Variant	rs72964028
Chromosome Location	chr3:52034746-52034747
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52034389..52038290-chr3:52040175..52043448,3	K562	blood:
2	chr3:52033669..52037332-chr3:52037907..52042194,5	K562	blood:
3	chr3:52028532..52031486-chr3:52034500..52037241,3	K562	blood:
4	chr3:52031889..52035644-chr3:52185003..52188385,3	K562	blood:
5	chr3:52028719..52032704-chr3:52033765..52037711,5	K562	blood:
6	chr3:52034176..52037779-chr3:52173821..52176492,3	K562	blood:
7	chr3:52034001..52035522-chr3:52089194..52091988,2	K562	blood:
8	chr3:52033103..52034881-chr3:52046794..52049765,2	K562	blood:
9	chr3:52034530..52036389-chr3:52177715..52178921,14	MCF-7	breast:
10	chr3:52033119..52035540-chr3:52073056..52074856,2	K562	blood:
11	chr3:52015868..52018375-chr3:52033679..52035628,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000114779	Chromatin interaction
ENSG00000164086	Chromatin interaction
ENSG00000243989	Chromatin interaction
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11916396	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2015691	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323861	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323871	0.90[AMR][1000 genomes]
rs323873	0.90[AMR][1000 genomes]
rs323874	0.90[AMR][1000 genomes]
rs323890	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.88[AFR][1000 genomes]
rs323897	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs72964029	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7432986	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers 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
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
11	nsv236961	chr3:52030637-52035392	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52030000-52035600	Weak transcription	Esophagus	oesophagus
2	chr3:52030200-52035400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:52030200-52035400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:52030200-52038600	Weak transcription	Fetal Kidney	kidney
5	chr3:52030400-52035400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:52030400-52035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:52030400-52035400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:52030400-52035400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:52030400-52035400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:52030400-52035400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:52030400-52035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:52030400-52035400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:52030400-52035400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52030400-52035400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:52030400-52035400	Weak transcription	Fetal Thymus	thymus
16	chr3:52030400-52035400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:52030400-52035600	Weak transcription	Primary B cells from cord blood	blood
18	chr3:52030400-52035600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:52030400-52035600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:52030400-52035600	Weak transcription	Fetal Intestine Small	intestine
21	chr3:52030400-52038200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:52030400-52039600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:52031600-52036000	Enhancers	K562	blood
24	chr3:52032200-52035800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:52032400-52035400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52032400-52035400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:52032400-52035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:52032400-52035400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:52032400-52035400	Weak transcription	Hela-S3	cervix
30	chr3:52032400-52035800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:52032400-52035800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:52032400-52035800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:52032400-52035800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:52032400-52035800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:52032400-52038600	Weak transcription	HUVEC	blood vessel
36	chr3:52032600-52035400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:52032600-52035800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:52033000-52034800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:52033000-52035400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:52033000-52035400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:52033000-52035400	Weak transcription	HMEC	breast
42	chr3:52033000-52035400	Weak transcription	NHEK	skin
43	chr3:52033000-52035600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:52033000-52035800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:52034200-52035800	Enhancers	Placenta	Placenta
46	chr3:52034400-52034800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:52034600-52035600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:52034600-52036000	Weak transcription	Placenta Amnion	Placenta Amnion

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