Variant report

Variant	rs13398989
Chromosome Location	chr2:172175068-172175069
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	chr2:172163945..172166501-chr2:172172840..172175232,2	MCF-7	breast:
2	chr2:172172855..172175323-chr2:172409152..172411417,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10454741	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11674632	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11679835	0.90[EUR][1000 genomes]
rs11687454	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11691073	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12105780	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12989392	0.84[EUR][1000 genomes]
rs12989938	0.84[EUR][1000 genomes]
rs12995219	0.83[AMR][1000 genomes]
rs13000846	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13002817	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13002867	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13003130	0.82[EUR][1000 genomes]
rs13005615	0.86[EUR][1000 genomes]
rs13023287	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13023973	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13031794	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2111459	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2356707	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34096402	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34787101	0.82[EUR][1000 genomes]
rs3731989	0.92[ASN][1000 genomes]
rs6722670	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7592018	0.98[AMR][1000 genomes];0.97[EUR][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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172163800-172181400	Weak transcription	Gastric	stomach
2	chr2:172165600-172179400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:172169200-172175600	Weak transcription	HepG2	liver
4	chr2:172169200-172178800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:172169200-172182400	Weak transcription	Aorta	Aorta
6	chr2:172169200-172193400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:172169400-172179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:172169600-172175200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:172169600-172179400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:172169800-172177200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:172169800-172181200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:172169800-172183200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:172170200-172192800	Weak transcription	Fetal Intestine Large	intestine
14	chr2:172170600-172178000	Weak transcription	Dnd41	blood
15	chr2:172170800-172175600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:172170800-172177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:172171000-172175200	Weak transcription	Primary T cells from cord blood	blood
18	chr2:172171000-172177400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:172171200-172175200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:172171200-172175200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:172171200-172178000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:172171400-172190800	Weak transcription	Esophagus	oesophagus
23	chr2:172171600-172176000	Weak transcription	K562	blood
24	chr2:172171800-172211600	Weak transcription	Fetal Intestine Small	intestine
25	chr2:172172000-172177600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:172172000-172177800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:172172200-172175400	Enhancers	Fetal Muscle Leg	muscle
28	chr2:172172400-172175200	Enhancers	Colon Smooth Muscle	Colon
29	chr2:172172400-172176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:172172400-172177200	Enhancers	Rectal Smooth Muscle	rectum
31	chr2:172172400-172177400	Enhancers	Brain Angular Gyrus	brain
32	chr2:172172400-172177400	Enhancers	Brain Cingulate Gyrus	brain
33	chr2:172172400-172177800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:172172400-172178000	Enhancers	Fetal Brain Male	brain
35	chr2:172172600-172175800	Weak transcription	HMEC	breast
36	chr2:172172600-172177600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr2:172172600-172177600	Weak transcription	Left Ventricle	heart
38	chr2:172172600-172179800	Weak transcription	Fetal Thymus	thymus
39	chr2:172172600-172190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:172172800-172190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:172172800-172222400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:172173000-172182200	Weak transcription	Liver	Liver
43	chr2:172173400-172175800	Enhancers	Primary B cells from peripheral blood	blood
44	chr2:172173600-172175200	Enhancers	Brain Anterior Caudate	brain
45	chr2:172173600-172175600	Enhancers	Brain Substantia Nigra	brain
46	chr2:172173600-172176000	Weak transcription	Placenta	Placenta
47	chr2:172173600-172186000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:172173800-172175200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr2:172173800-172175200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:172173800-172176400	Flanking Active TSS	GM12878-XiMat	blood

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