Variant report

Variant	rs55854246
Chromosome Location	chr2:73336665-73336666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr2:73336338-73337205	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr2:73332373-73337395	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73332810..73335767-chr2:73335850..73338360,4	K562	blood:
2	chr2:73336661..73339816-chr2:73350346..73353019,4	K562	blood:
3	chr2:73324923..73326792-chr2:73335273..73337149,2	K562	blood:
4	chr2:73330344..73333243-chr2:73334640..73337340,3	MCF-7	breast:
5	chr2:73295259..73298066-chr2:73336566..73338482,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272702	TF binding region
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17348624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17348638	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17433172	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17504663	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17504810	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17511570	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17570040	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17570432	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4143146	0.99[ASN][1000 genomes]
rs55633543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55768189	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55801301	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55881165	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55938508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56026282	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56088054	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56161051	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56214999	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56280862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57522927	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57666506	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57868938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6706065	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73943009	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73943014	0.85[EUR][1000 genomes]
rs73943015	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73943016	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73943017	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73943034	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73943035	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73943036	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73943408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73943410	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73945731	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73945733	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73945734	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73945735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73945740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73315600-73338000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:73316200-73338400	Weak transcription	Brain Germinal Matrix	brain
3	chr2:73327000-73338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:73329400-73338200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:73329600-73337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:73329800-73337800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:73330400-73337400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:73330400-73337400	Weak transcription	Fetal Lung	lung
9	chr2:73330600-73337800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:73330800-73336800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:73330800-73337800	Enhancers	Placenta	Placenta
12	chr2:73330800-73338200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:73331200-73337000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:73331200-73337600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:73331200-73337600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:73331400-73337200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:73332400-73337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:73332800-73337200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:73332800-73337400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:73333800-73337800	Enhancers	HepG2	liver
21	chr2:73334600-73338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:73334800-73337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:73334800-73337400	Enhancers	Brain Angular Gyrus	brain
24	chr2:73334800-73337800	Weak transcription	Fetal Brain Female	brain
25	chr2:73335000-73337000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:73335000-73337200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:73335000-73337200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:73335000-73337200	Weak transcription	HMEC	breast
29	chr2:73335000-73338200	Weak transcription	Stomach Mucosa	stomach
30	chr2:73335200-73336800	Weak transcription	Gastric	stomach
31	chr2:73335200-73336800	Weak transcription	Left Ventricle	heart
32	chr2:73335200-73337000	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:73335200-73337400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:73335200-73337400	Weak transcription	Adipose Nuclei	Adipose
35	chr2:73335200-73337400	Weak transcription	Colonic Mucosa	Colon
36	chr2:73335200-73337400	Weak transcription	Esophagus	oesophagus
37	chr2:73335200-73337400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:73335200-73337800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:73335200-73337800	Weak transcription	Aorta	Aorta
40	chr2:73335200-73337800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:73335200-73337800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:73335400-73337200	Weak transcription	Fetal Intestine Small	intestine
43	chr2:73335400-73337200	Weak transcription	Osteobl	bone
44	chr2:73335400-73338000	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:73335400-73338200	Weak transcription	Brain Substantia Nigra	brain
46	chr2:73335600-73336800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:73335600-73336800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:73335600-73337000	Weak transcription	NHLF	lung
49	chr2:73335600-73337200	Weak transcription	Ovary	ovary
50	chr2:73335600-73337400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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