Variant report

Variant	rs28783173
Chromosome Location	chr2:99336608-99336609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99336480..99339286-chr2:99347871..99349769,2	MCF-7	breast:
2	chr2:99329459..99332003-chr2:99335709..99337859,2	MCF-7	breast:
3	chr2:99334922..99337052-chr2:99339872..99343548,3	MCF-7	breast:
4	chr2:99334681..99338238-chr2:99344696..99347399,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1016124	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173832	0.80[ASN][1000 genomes]
rs10174321	0.81[ASN][1000 genomes]
rs10177696	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10194177	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10199267	0.81[EUR][1000 genomes]
rs10200288	0.92[ASN][1000 genomes]
rs10210711	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10460485	0.81[EUR][1000 genomes]
rs10496332	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123747	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11123749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123751	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885883	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12471383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477450	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615301	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622931	0.81[EUR][1000 genomes]
rs12993424	0.94[ASN][1000 genomes]
rs13391483	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391794	0.81[EUR][1000 genomes]
rs13410406	0.81[EUR][1000 genomes]
rs1514916	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1517681	0.94[ASN][1000 genomes]
rs1913621	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013983	0.94[ASN][1000 genomes]
rs34521960	0.94[ASN][1000 genomes]
rs35477458	0.94[ASN][1000 genomes]
rs41445250	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851150	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851153	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851154	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58666702	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60024860	0.81[EUR][1000 genomes]
rs6733957	0.81[EUR][1000 genomes]
rs6737760	0.81[EUR][1000 genomes]
rs6740656	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7420869	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558236	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7577636	0.81[EUR][1000 genomes]
rs7599792	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99319200-99336800	Weak transcription	Spleen	Spleen
2	chr2:99322000-99336800	Weak transcription	Colonic Mucosa	Colon
3	chr2:99325600-99336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:99326400-99336800	Weak transcription	Aorta	Aorta
5	chr2:99326400-99342600	Weak transcription	Adipose Nuclei	Adipose
6	chr2:99326400-99343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:99326400-99346400	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:99326600-99336800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:99326600-99336800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:99326600-99336800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:99326600-99340000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:99326800-99336800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:99326800-99337000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:99326800-99342600	Weak transcription	Liver	Liver
15	chr2:99326800-99343800	Weak transcription	Small Intestine	intestine
16	chr2:99327200-99336800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:99328400-99336800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:99328600-99336800	Weak transcription	Left Ventricle	heart
19	chr2:99328800-99337000	Weak transcription	Psoas Muscle	Psoas
20	chr2:99329600-99339600	Weak transcription	Right Atrium	heart
21	chr2:99331200-99337400	Weak transcription	HUVEC	blood vessel
22	chr2:99332600-99337200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:99333000-99342800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:99333400-99337400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:99334000-99339400	Strong transcription	Dnd41	blood
26	chr2:99334200-99343200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr2:99334400-99339400	Weak transcription	Esophagus	oesophagus
28	chr2:99334800-99337200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:99335200-99336800	Weak transcription	HepG2	liver
30	chr2:99335200-99343600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:99335200-99346600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:99335400-99336800	Weak transcription	Lung	lung
33	chr2:99335400-99342800	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:99335400-99343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:99335600-99336800	Weak transcription	Pancreas	Pancrea
36	chr2:99335600-99336800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:99335600-99336800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:99335600-99339600	Weak transcription	Gastric	stomach
39	chr2:99335600-99343200	Strong transcription	Fetal Thymus	thymus
40	chr2:99335600-99345800	Weak transcription	Right Ventricle	heart
41	chr2:99335800-99339800	Weak transcription	Brain Substantia Nigra	brain
42	chr2:99336000-99336800	Weak transcription	Thymus	Thymus
43	chr2:99336200-99337000	ZNF genes & repeats	Fetal Stomach	stomach
44	chr2:99336200-99337800	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr2:99336200-99337800	ZNF genes & repeats	Fetal Intestine Small	intestine
46	chr2:99336400-99336800	Weak transcription	Primary T cells from cord blood	blood
47	chr2:99336400-99336800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:99336400-99336800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:99336400-99336800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:99336400-99336800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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