Variant report

Variant	rs60139983
Chromosome Location	chr3:105574260-105574261
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105567530..105570429-chr3:105573055..105575422,2	MCF-7	breast:
2	chr3:105553976..105556329-chr3:105573888..105575863,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12491881	1.00[EUR][1000 genomes]
rs1503922	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844739	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851406	1.00[EUR][1000 genomes]
rs16851428	1.00[EUR][1000 genomes]
rs16851443	1.00[EUR][1000 genomes]
rs16851470	1.00[EUR][1000 genomes]
rs16851492	1.00[EUR][1000 genomes]
rs16851534	1.00[EUR][1000 genomes]
rs2055561	0.84[EUR][1000 genomes]
rs2055562	1.00[EUR][1000 genomes]
rs2134716	0.84[EUR][1000 genomes]
rs2134717	0.84[EUR][1000 genomes]
rs2301039	1.00[EUR][1000 genomes]
rs3772535	1.00[EUR][1000 genomes]
rs57292140	0.92[EUR][1000 genomes]
rs57856850	1.00[EUR][1000 genomes]
rs58424957	1.00[EUR][1000 genomes]
rs59184166	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59197939	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59358778	1.00[EUR][1000 genomes]
rs59523739	1.00[EUR][1000 genomes]
rs59569585	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59612207	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60536875	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60737645	0.92[EUR][1000 genomes]
rs61317978	1.00[EUR][1000 genomes]
rs7622735	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920711	1.00[EUR][1000 genomes];1.00[ASN][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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105543400-105581200	Weak transcription	Gastric	stomach
2	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
4	chr3:105555800-105576600	Weak transcription	Psoas Muscle	Psoas
5	chr3:105556200-105579000	Weak transcription	Stomach Mucosa	stomach
6	chr3:105557800-105579200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:105562000-105586000	Weak transcription	K562	blood
11	chr3:105563000-105584600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:105563400-105583000	Weak transcription	Spleen	Spleen
14	chr3:105563800-105584400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:105565600-105584800	Weak transcription	NHEK	skin
17	chr3:105566000-105574800	Strong transcription	Placenta	Placenta
18	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:105566600-105581200	Weak transcription	Aorta	Aorta
21	chr3:105566600-105584600	Weak transcription	Fetal Stomach	stomach
22	chr3:105567000-105576600	Weak transcription	Right Ventricle	heart
23	chr3:105567000-105578800	Weak transcription	Fetal Brain Male	brain
24	chr3:105567000-105583000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:105567000-105584200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:105567200-105576600	Weak transcription	Ovary	ovary
27	chr3:105567200-105583200	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:105567200-105584000	Weak transcription	Brain Anterior Caudate	brain
29	chr3:105567200-105584600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:105567600-105574600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:105567800-105575400	Strong transcription	NH-A	brain
32	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
34	chr3:105568400-105574400	Strong transcription	Fetal Lung	lung
35	chr3:105568400-105576000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:105568400-105576800	Weak transcription	Small Intestine	intestine
37	chr3:105568600-105579600	Strong transcription	Osteobl	bone
38	chr3:105568800-105579200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
40	chr3:105569200-105574600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:105569400-105574400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr3:105569400-105576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:105569400-105584000	Weak transcription	A549	lung
44	chr3:105569600-105574400	Strong transcription	Liver	Liver
45	chr3:105569600-105574600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr3:105569600-105574600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:105569600-105574600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:105569600-105574600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:105569600-105574600	Strong transcription	Fetal Muscle Leg	muscle
50	chr3:105569600-105579600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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