Variant report

Variant	rs11688098
Chromosome Location	chr2:20185708-20185709
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20184304..20186440-chr2:20187724..20190489,3	MCF-7	breast:
2	chr2:20182746..20185728-chr2:20188193..20192191,4	K562	blood:
3	chr2:20168703..20170749-chr2:20184154..20185813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1056233	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1115275	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680554	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11681705	0.85[AMR][1000 genomes]
rs11683973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11688680	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11693384	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11694821	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12986437	0.85[AMR][1000 genomes]
rs12988913	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12990087	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12995324	0.81[AMR][1000 genomes]
rs12996974	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13001254	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13005512	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13006748	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13011870	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13035048	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370585	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16987220	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16987257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17695872	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1921731	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992167	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2028208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28452699	0.85[AMR][1000 genomes]
rs34400777	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34425205	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34459327	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34595677	0.81[AMR][1000 genomes]
rs34741640	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35307726	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35425971	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35973216	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4294960	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66496755	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706311	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6720011	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67653248	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67724270	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67915887	0.85[AMR][1000 genomes]
rs721932	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721933	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73214266	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs957614	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][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	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
4	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:20157800-20187200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:20164600-20187000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
19	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr2:20165000-20187000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:20165000-20188400	Weak transcription	K562	blood
22	chr2:20165400-20187600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:20165800-20188200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:20169000-20188800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:20169000-20189000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:20169200-20188800	Weak transcription	Right Ventricle	heart
27	chr2:20171800-20187800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:20172000-20188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:20174000-20188800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:20174000-20189000	Weak transcription	Fetal Intestine Small	intestine
31	chr2:20174200-20189400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:20174400-20188800	Weak transcription	Fetal Stomach	stomach
33	chr2:20174400-20189200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:20174800-20189200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:20175200-20188800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:20175200-20188800	Weak transcription	Liver	Liver
37	chr2:20175800-20188800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:20177000-20188000	Weak transcription	Thymus	Thymus
39	chr2:20177200-20188800	Weak transcription	HSMMtube	muscle
40	chr2:20177800-20187800	Weak transcription	Brain Anterior Caudate	brain
41	chr2:20177800-20187800	Weak transcription	Fetal Brain Female	brain
42	chr2:20177800-20188200	Weak transcription	Brain Germinal Matrix	brain
43	chr2:20177800-20188200	Weak transcription	Fetal Brain Male	brain
44	chr2:20177800-20188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:20177800-20188800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:20177800-20189000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:20178000-20187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:20178000-20187800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:20178000-20187800	Weak transcription	HMEC	breast
50	chr2:20178000-20188000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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