Variant report

Variant	rs11688680
Chromosome Location	chr2:20133473-20133474
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20128853..20131612-chr2:20133463..20134985,2	K562	blood:
2	chr2:20099946..20102449-chr2:20132225..20134655,2	MCF-7	breast:
3	chr2:20131153..20134079-chr2:20137920..20140711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1056233	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1115275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683973	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688098	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11693384	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11694821	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12988913	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990087	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12996974	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001254	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006748	0.93[ASN][1000 genomes]
rs13011870	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035048	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1370585	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987220	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987257	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1921731	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1992167	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028208	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34400777	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34425205	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34459327	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35307726	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35425971	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35973216	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4294960	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496755	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706311	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720011	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67653248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67724270	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721932	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs721933	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214266	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs957614	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[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	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
3	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:20121600-20135800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:20123400-20135800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:20126400-20137200	Weak transcription	Colonic Mucosa	Colon
9	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:20127600-20139200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:20127800-20135800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:20128000-20137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:20128000-20139200	Weak transcription	Pancreas	Pancrea
14	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
16	chr2:20128600-20133600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr2:20128600-20136000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:20129000-20135400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:20129400-20135600	Weak transcription	Primary T cells from cord blood	blood
20	chr2:20129400-20135800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:20129400-20135800	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:20129400-20135800	Weak transcription	Fetal Thymus	thymus
23	chr2:20129400-20138600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:20129400-20143000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:20129400-20144000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
27	chr2:20129600-20136000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:20129600-20138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
30	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:20129800-20134000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:20130200-20136000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:20130400-20135200	Weak transcription	Adipose Nuclei	Adipose
35	chr2:20130400-20135400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:20130400-20135800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:20130400-20135800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:20130400-20136000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:20130400-20136000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:20130400-20136200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:20130400-20140200	Weak transcription	Liver	Liver
42	chr2:20130400-20141800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:20130400-20142000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:20130400-20142600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:20130400-20149400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:20130400-20149400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:20130400-20164600	Weak transcription	Lung	lung
48	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:20130600-20135200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:20130600-20135200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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