Variant report

Variant	rs12477699
Chromosome Location	chr2:173245726-173245727
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173241953..173243647-chr2:173245498..173247532,2	MCF-7	breast:
2	chr2:173238964..173242268-chr2:173243569..173246875,3	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10207752	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10930552	0.95[EUR][1000 genomes]
rs10930553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677757	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687888	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997279	0.80[AMR][1000 genomes]
rs13020542	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027402	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13028213	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4972814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972817	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972818	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173239200-173260200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173243800-173246800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:173243800-173247400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:173244400-173247000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:173244400-173247200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:173244600-173245800	Enhancers	Fetal Muscle Trunk	muscle
7	chr2:173244600-173254400	Weak transcription	Lung	lung
8	chr2:173244800-173246400	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:173244800-173246400	Enhancers	Fetal Intestine Large	intestine
10	chr2:173244800-173246400	Enhancers	Spleen	Spleen
11	chr2:173244800-173246600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:173244800-173246600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:173244800-173246600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:173244800-173247600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:173245000-173245800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr2:173245000-173245800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:173245000-173245800	Enhancers	HUVEC	blood vessel
18	chr2:173245000-173246200	Enhancers	Fetal Intestine Small	intestine
19	chr2:173245000-173246200	Enhancers	HSMMtube	muscle
20	chr2:173245000-173246400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:173245000-173246400	Enhancers	Fetal Lung	lung
22	chr2:173245000-173247600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr2:173245200-173245800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:173245200-173246000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr2:173245200-173246000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:173245200-173246200	Enhancers	Adipose Nuclei	Adipose
27	chr2:173245200-173246200	Enhancers	Fetal Muscle Leg	muscle
28	chr2:173245200-173246400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:173245200-173246400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:173245200-173246400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:173245200-173246400	Enhancers	Fetal Thymus	thymus
32	chr2:173245200-173246400	Enhancers	Stomach Mucosa	stomach
33	chr2:173245200-173246600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr2:173245200-173246600	Enhancers	Fetal Heart	heart
35	chr2:173245200-173246600	Enhancers	Fetal Stomach	stomach
36	chr2:173245200-173246600	Enhancers	Ovary	ovary
37	chr2:173245400-173245800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:173245400-173245800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:173245400-173245800	Weak transcription	Pancreas	Pancrea
40	chr2:173245400-173246000	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:173245400-173246000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:173245400-173246200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:173245400-173246200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:173245400-173246200	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:173245400-173246200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr2:173245400-173246200	Enhancers	NH-A	brain
47	chr2:173245400-173246400	Enhancers	Fetal Kidney	kidney
48	chr2:173245400-173246400	Enhancers	Left Ventricle	heart
49	chr2:173245400-173247200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:173245400-173248000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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