Variant report

Variant	rs72953404
Chromosome Location	chr3:51668298-51668299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51534170..51537061-chr3:51667512..51669238,2	MCF-7	breast:
2	chr3:51663530..51666106-chr3:51668183..51670833,2	K562	blood:

Variant related genes	Relation type
ENSG00000164080	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1480366	1.00[AMR][1000 genomes]
rs17051802	1.00[AMR][1000 genomes]
rs4280628	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4555511	1.00[AMR][1000 genomes]
rs57019473	1.00[AMR][1000 genomes]
rs58075772	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58807639	1.00[AMR][1000 genomes]
rs59307262	1.00[AMR][1000 genomes]
rs60497133	1.00[AMR][1000 genomes]
rs61452834	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72945711	1.00[AMR][1000 genomes]
rs72945738	1.00[AMR][1000 genomes]
rs72945741	1.00[AMR][1000 genomes]
rs72951454	1.00[AMR][1000 genomes]
rs72951466	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951469	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951474	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951478	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72951489	1.00[AMR][1000 genomes]
rs72953419	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72953421	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs880477	1.00[AMR][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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:51655600-51671800	Weak transcription	K562	blood
2	chr3:51655800-51680200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:51656000-51669200	Weak transcription	A549	lung
4	chr3:51656000-51673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:51656800-51671200	Weak transcription	Stomach Mucosa	stomach
6	chr3:51657200-51671200	Weak transcription	Psoas Muscle	Psoas
7	chr3:51657600-51669000	Weak transcription	NHDF-Ad	bronchial
8	chr3:51660000-51669600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:51660800-51671000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:51660800-51680200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:51660800-51681000	Strong transcription	HepG2	liver
12	chr3:51660800-51681400	Strong transcription	Primary T cells from cord blood	blood
13	chr3:51660800-51681800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:51660800-51683000	Strong transcription	Primary B cells from cord blood	blood
15	chr3:51660800-51683200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:51661000-51670600	Strong transcription	Liver	Liver
17	chr3:51661000-51671200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:51661000-51676600	Strong transcription	Adipose Nuclei	Adipose
19	chr3:51661000-51679600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:51661000-51680200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:51661000-51680400	Strong transcription	Dnd41	blood
22	chr3:51661000-51682600	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:51661000-51682600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:51661000-51682600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:51661000-51683000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:51661000-51684200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:51661200-51680600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:51661200-51680600	Strong transcription	Thymus	Thymus
29	chr3:51661200-51681200	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:51661200-51681800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:51661200-51682600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:51661200-51683000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:51661200-51683000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr3:51661400-51668800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:51661400-51680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:51661400-51681200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:51661400-51681800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:51661400-51681800	Strong transcription	Lung	lung
39	chr3:51661400-51682600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:51661400-51682600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:51661400-51682800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:51661400-51683000	Strong transcription	Brain Hippocampus Middle	brain
43	chr3:51661600-51669000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:51661600-51670400	Strong transcription	Placenta	Placenta
45	chr3:51661600-51671000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr3:51661600-51676400	Strong transcription	Fetal Brain Female	brain
47	chr3:51661600-51679800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:51661600-51681600	Strong transcription	Fetal Stomach	stomach
49	chr3:51661600-51681800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:51661600-51682000	Strong transcription	Fetal Thymus	thymus

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