Variant report

Variant	rs72964029
Chromosome Location	chr3:52036760-52036761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr3:52035823..52039676-chr3:52176607..52179905,3	K562	blood:
5	chr3:52028719..52032704-chr3:52033765..52037711,5	K562	blood:
6	chr3:52034176..52037779-chr3:52173821..52176492,3	K562	blood:
7	chr3:52036196..52037192-chr3:52156747..52157405,2	K562	blood:

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11916396	1.00[ASN][1000 genomes]
rs2015691	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	1.00[ASN][1000 genomes]
rs323861	1.00[ASN][1000 genomes]
rs323862	1.00[ASN][1000 genomes]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323871	0.80[AMR][1000 genomes]
rs323873	0.80[AMR][1000 genomes]
rs323874	0.80[AMR][1000 genomes]
rs323890	1.00[ASN][1000 genomes]
rs323892	1.00[ASN][1000 genomes]
rs323897	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	1.00[ASN][1000 genomes]
rs404527	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.80[AMR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs72964028	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52030200-52038600	Weak transcription	Fetal Kidney	kidney
2	chr3:52030400-52038200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:52030400-52039600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:52032400-52038600	Weak transcription	HUVEC	blood vessel
5	chr3:52035400-52037600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr3:52035400-52041800	Enhancers	Fetal Muscle Leg	muscle
7	chr3:52035600-52037000	Enhancers	Fetal Brain Male	brain
8	chr3:52035600-52038800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52035600-52039200	Weak transcription	Colonic Mucosa	Colon
10	chr3:52035800-52036800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:52035800-52037200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:52035800-52037600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:52035800-52038800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52035800-52039200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:52035800-52039400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:52035800-52041200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:52036000-52036800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
18	chr3:52036000-52037200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr3:52036000-52038000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:52036000-52038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:52036000-52038000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:52036000-52038200	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52036000-52038200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:52036000-52038200	Weak transcription	Esophagus	oesophagus
25	chr3:52036000-52038200	Weak transcription	Left Ventricle	heart
26	chr3:52036000-52038200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:52036000-52038200	Weak transcription	HMEC	breast
28	chr3:52036000-52038400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:52036000-52038400	Weak transcription	Adipose Nuclei	Adipose
30	chr3:52036000-52038400	Weak transcription	Fetal Heart	heart
31	chr3:52036000-52038400	Weak transcription	Fetal Intestine Large	intestine
32	chr3:52036000-52038400	Weak transcription	Fetal Intestine Small	intestine
33	chr3:52036000-52038400	Weak transcription	NHLF	lung
34	chr3:52036000-52038600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:52036000-52038600	Weak transcription	K562	blood
36	chr3:52036000-52038800	Weak transcription	Ovary	ovary
37	chr3:52036000-52039000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52036000-52039200	Weak transcription	Stomach Mucosa	stomach
39	chr3:52036000-52039400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:52036000-52039400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:52036000-52039400	Weak transcription	Liver	Liver
42	chr3:52036000-52039400	Weak transcription	Gastric	stomach
43	chr3:52036000-52039400	Weak transcription	Psoas Muscle	Psoas
44	chr3:52036000-52039600	Weak transcription	GM12878-XiMat	blood
45	chr3:52036000-52039800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:52036000-52040000	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:52036200-52037800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:52036200-52038000	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:52036200-52038000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:52036200-52038200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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