Variant report

Variant	rs12860399
Chromosome Location	chr13:48529003-48529004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12864691	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17425881	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2031591	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2296573	0.87[EUR][1000 genomes]
rs7981260	0.85[EUR][1000 genomes]
rs8001871	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9567965	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9567968	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
2	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
5	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
6	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:48508600-48530800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:48509000-48530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:48511000-48530600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
12	chr13:48511800-48531200	Weak transcription	HUVEC	blood vessel
13	chr13:48512200-48530000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:48512200-48530800	Weak transcription	Colonic Mucosa	Colon
15	chr13:48512200-48531200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:48512600-48529400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:48512600-48530800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:48512600-48531400	Weak transcription	Aorta	Aorta
19	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
20	chr13:48512800-48531200	Weak transcription	Gastric	stomach
21	chr13:48512800-48533800	Weak transcription	NHLF	lung
22	chr13:48513000-48530400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr13:48513000-48531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:48513600-48530000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr13:48516200-48531200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:48516400-48529600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:48516800-48529200	Weak transcription	Fetal Intestine Small	intestine
29	chr13:48516800-48529400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:48517000-48530600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr13:48517800-48530400	Weak transcription	HMEC	breast
32	chr13:48519600-48529400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr13:48519600-48529600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr13:48519600-48530000	Strong transcription	Dnd41	blood
35	chr13:48519600-48531200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr13:48519600-48533800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:48520000-48529200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:48520000-48529400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:48520000-48530400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:48520200-48530400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:48521000-48529200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr13:48521200-48530000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:48521600-48529200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr13:48522000-48530600	Strong transcription	Adipose Nuclei	Adipose
45	chr13:48522200-48529200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr13:48522200-48529800	Strong transcription	Fetal Lung	lung
47	chr13:48522600-48529800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:48522800-48530200	Strong transcription	Primary T cells from cord blood	blood
49	chr13:48523000-48541600	Weak transcription	Psoas Muscle	Psoas
50	chr13:48523000-48542600	Weak transcription	K562	blood

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