Variant report

Variant	rs7650089
Chromosome Location	chr3:160820401-160820402
allele	A/C
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	MAX	chr3:160820366-160820667	NB4	blood:	n/a	chr3:160820498-160820508 chr3:160820479-160820490 chr3:160820479-160820490 chr3:160820480-160820489 chr3:160820480-160820490 chr3:160820481-160820488

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160819385..160821536-chr3:161081853..161083436,2	MCF-7	breast:
3	chr3:160819969..160822199-chr3:161125222..161127254,2	MCF-7	breast:
4	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
5	chr3:160819564..160821281-chr3:160942870..160944755,2	MCF-7	breast:

Variant related genes	Relation type
B3GALNT1	TF binding region
NMD3	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2231256	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34184112	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34727550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35904210	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35961258	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv877705	chr3:160818188-160836006	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877706	chr3:160820175-160826404	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877707	chr3:160820175-160836006	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
2	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
3	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:160799800-160821800	Weak transcription	NHLF	lung
8	chr3:160799800-160822000	Weak transcription	HMEC	breast
9	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
11	chr3:160801000-160821800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:160801200-160822000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:160801600-160821800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:160802600-160821400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:160802600-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:160802800-160822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:160803400-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:160803800-160822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:160804400-160822000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:160804400-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:160804600-160821800	Weak transcription	Brain Substantia Nigra	brain
23	chr3:160804600-160821800	Weak transcription	HUVEC	blood vessel
24	chr3:160804600-160822200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:160809000-160821800	Weak transcription	NHDF-Ad	bronchial
26	chr3:160809000-160822200	Weak transcription	Psoas Muscle	Psoas
27	chr3:160813400-160822000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:160814000-160821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:160814600-160820800	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:160815200-160820800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:160815200-160820800	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr3:160815600-160821400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:160815800-160820800	Strong transcription	Fetal Lung	lung
34	chr3:160816000-160821000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:160816000-160822200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:160816200-160820800	Strong transcription	Ovary	ovary
37	chr3:160816400-160820600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr3:160816400-160820800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:160816600-160820800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:160816800-160821000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:160817000-160821200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:160817200-160820600	Strong transcription	Brain Anterior Caudate	brain
43	chr3:160817200-160820800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:160817200-160820800	Strong transcription	Osteobl	bone
45	chr3:160817200-160822000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:160817400-160821000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:160817400-160822000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:160817800-160822000	Weak transcription	NHEK	skin
49	chr3:160818600-160821000	Strong transcription	Fetal Stomach	stomach
50	chr3:160818800-160820800	Strong transcription	Brain Germinal Matrix	brain

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