Variant report

Variant	rs2309825
Chromosome Location	chr2:100905101-100905102
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100889401..100893026-chr2:100904259..100909793,5	MCF-7	breast:
2	chr2:100900693..100917248-chr2:100932005..100942326,51	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10865038	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865039	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123825	0.82[EUR][1000 genomes]
rs12464505	1.00[JPT][hapmap]
rs12467008	1.00[JPT][hapmap]
rs13008568	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13024601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13031270	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13031493	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13031712	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13033057	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2033748	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2033749	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2309815	1.00[JPT][hapmap]
rs2309817	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309818	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309819	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309820	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2309821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309822	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309823	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309824	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2309826	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2871341	1.00[JPT][hapmap]
rs4851281	1.00[JPT][hapmap]
rs4851282	1.00[JPT][hapmap]
rs4851284	0.82[EUR][1000 genomes]
rs4851285	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4851286	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4851287	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6542923	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542924	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6754867	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6755791	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7421891	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7557575	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7557660	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7557977	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7559464	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7562372	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7582180	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7588623	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7601442	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7601873	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7606277	0.86[EUR][1000 genomes]
rs7607170	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7607676	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7609376	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:100896600-100907000	Weak transcription	Spleen	Spleen
4	chr2:100896600-100907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:100898400-100906800	Weak transcription	Placenta	Placenta
6	chr2:100898400-100908200	Weak transcription	Fetal Lung	lung
7	chr2:100898400-100915600	Weak transcription	Right Atrium	heart
8	chr2:100898800-100915000	Weak transcription	Adipose Nuclei	Adipose
9	chr2:100899000-100907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:100900000-100905600	Strong transcription	Aorta	Aorta
11	chr2:100900200-100905200	Strong transcription	Brain Germinal Matrix	brain
12	chr2:100900200-100919000	Strong transcription	Fetal Brain Female	brain
13	chr2:100900800-100906800	Weak transcription	Fetal Thymus	thymus
14	chr2:100900800-100907000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:100900800-100907800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:100900800-100926600	Weak transcription	Right Ventricle	heart
17	chr2:100901000-100937000	Weak transcription	Fetal Brain Male	brain
18	chr2:100901600-100907200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr2:100902200-100907000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:100902400-100906400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:100902400-100907000	Weak transcription	Lung	lung
22	chr2:100902400-100907400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:100902400-100908000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:100902600-100907400	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:100902600-100907600	Weak transcription	Fetal Stomach	stomach
26	chr2:100903000-100906400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:100903000-100907000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:100903000-100907200	Weak transcription	Esophagus	oesophagus
29	chr2:100903000-100907600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:100903200-100907000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:100903200-100907200	Weak transcription	HUVEC	blood vessel
32	chr2:100903200-100907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:100903200-100918000	Weak transcription	Liver	Liver
34	chr2:100903400-100906800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:100903400-100907200	Weak transcription	Fetal Intestine Small	intestine
36	chr2:100903400-100907400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:100903400-100907600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:100903400-100907600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:100903400-100909400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:100903400-100930800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:100903600-100905200	Strong transcription	A549	lung
42	chr2:100903600-100905600	Weak transcription	Left Ventricle	heart
43	chr2:100903600-100906200	Weak transcription	Brain Angular Gyrus	brain
44	chr2:100903600-100906400	Weak transcription	Dnd41	blood
45	chr2:100903600-100906600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:100903600-100906600	Weak transcription	Hela-S3	cervix
47	chr2:100903600-100906800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:100903600-100906800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:100903600-100907000	Weak transcription	Stomach Mucosa	stomach
50	chr2:100903600-100907800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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