Variant report

Variant	rs10460485
Chromosome Location	chr2:99330711-99330712
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	chr2:99329459..99332003-chr2:99335709..99337859,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1016124	0.81[EUR][1000 genomes]
rs10177696	0.88[EUR][1000 genomes]
rs10194177	0.87[EUR][1000 genomes]
rs10199267	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10496332	0.81[EUR][1000 genomes]
rs11123747	0.81[EUR][1000 genomes]
rs11123749	0.81[EUR][1000 genomes]
rs12471383	0.81[EUR][1000 genomes]
rs12477450	0.88[EUR][1000 genomes]
rs12615301	0.81[EUR][1000 genomes]
rs12622931	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13391483	0.81[EUR][1000 genomes]
rs13391794	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13410406	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13428808	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1514916	0.88[EUR][1000 genomes]
rs1913621	0.81[EUR][1000 genomes]
rs28783173	0.81[EUR][1000 genomes]
rs41445250	0.88[EUR][1000 genomes]
rs4851150	0.81[EUR][1000 genomes]
rs4851154	0.81[EUR][1000 genomes]
rs58666702	0.88[EUR][1000 genomes]
rs60024860	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706340	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6729151	0.83[EUR][1000 genomes]
rs6733957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6737760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6740656	0.83[EUR][1000 genomes]
rs6751196	0.87[EUR][1000 genomes]
rs7420869	0.83[EUR][1000 genomes]
rs7558236	0.81[EUR][1000 genomes]
rs7577636	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599792	0.81[EUR][1000 genomes]
rs7601040	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99303200-99336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:99316600-99336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:99319200-99336800	Weak transcription	Spleen	Spleen
4	chr2:99321000-99336200	Weak transcription	Fetal Stomach	stomach
5	chr2:99321200-99335000	Weak transcription	Lung	lung
6	chr2:99321600-99336600	Weak transcription	Fetal Kidney	kidney
7	chr2:99322000-99332600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:99322000-99334000	Weak transcription	Dnd41	blood
9	chr2:99322000-99336800	Weak transcription	Colonic Mucosa	Colon
10	chr2:99322200-99336200	Weak transcription	Fetal Intestine Large	intestine
11	chr2:99324200-99336600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:99325400-99331000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:99325400-99333400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr2:99325600-99336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:99325800-99334200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:99326400-99336000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:99326400-99336800	Weak transcription	Aorta	Aorta
18	chr2:99326400-99342600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:99326400-99343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:99326400-99346400	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:99326600-99330800	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:99326600-99334200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:99326600-99336800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:99326600-99336800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:99326600-99336800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:99326600-99340000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:99326800-99330800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:99326800-99332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:99326800-99335000	Weak transcription	Brain Substantia Nigra	brain
30	chr2:99326800-99336600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:99326800-99336600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:99326800-99336800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:99326800-99337000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:99326800-99342600	Weak transcription	Liver	Liver
35	chr2:99326800-99343800	Weak transcription	Small Intestine	intestine
36	chr2:99327200-99336800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:99327600-99331200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:99327600-99333000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:99327600-99335000	Weak transcription	Right Ventricle	heart
40	chr2:99327800-99331400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr2:99327800-99334200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:99327800-99336000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr2:99328000-99335600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr2:99328400-99332000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:99328400-99333000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:99328400-99336600	Weak transcription	Primary B cells from cord blood	blood
47	chr2:99328400-99336800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:99328600-99336600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:99328600-99336800	Weak transcription	Left Ventricle	heart
50	chr2:99328800-99331000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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