Variant report

Variant	rs138660
Chromosome Location	chr22:28404006-28404007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28401032..28403259-chr22:28403789..28405576,2	K562	blood:
2	chr22:28393472..28395855-chr22:28403235..28405878,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28402517-28404569	ENSG00000235954

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10154425	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs10212007	0.84[EUR][1000 genomes]
rs10212036	0.86[EUR][1000 genomes]
rs10483140	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10483142	0.88[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483143	0.88[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs118840	0.89[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165651	0.93[EUR][1000 genomes]
rs12165797	0.93[EUR][1000 genomes]
rs12166023	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs12166077	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166158	0.95[EUR][1000 genomes]
rs12166164	0.86[EUR][1000 genomes]
rs12166256	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166389	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs12166719	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166740	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166912	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs12166938	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167128	0.89[MEX][hapmap]
rs12167320	0.93[EUR][1000 genomes]
rs12167829	0.93[EUR][1000 genomes]
rs12168054	1.00[CEU][hapmap];0.80[YRI][hapmap];0.96[EUR][1000 genomes]
rs12168180	0.89[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168251	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168582	0.89[CEU][hapmap];0.89[MEX][hapmap];0.91[EUR][1000 genomes]
rs12169097	0.93[EUR][1000 genomes]
rs12169888	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12169936	0.93[EUR][1000 genomes]
rs12170022	0.95[EUR][1000 genomes]
rs12170558	0.88[CEU][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170953	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171104	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs130414	0.89[MEX][hapmap]
rs138636	0.89[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138637	0.89[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138639	0.89[CEU][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138640	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138642	0.89[CEU][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138646	0.89[MEX][hapmap];0.91[YRI][hapmap]
rs138648	0.89[CEU][hapmap]
rs138651	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138653	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138654	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138656	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138658	1.00[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138665	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138667	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138669	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138670	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138671	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138672	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138676	0.89[CEU][hapmap]
rs138679	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs138680	0.89[CEU][hapmap]
rs16985763	0.93[EUR][1000 genomes]
rs16985967	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985976	0.86[EUR][1000 genomes]
rs16986037	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16986077	0.89[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs16987005	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs17390800	0.93[EUR][1000 genomes]
rs17407024	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17483887	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17484337	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143420	0.89[MEX][hapmap];0.89[YRI][hapmap]
rs2745562	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375646	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28579300	0.82[EUR][1000 genomes]
rs4036493	0.84[EUR][1000 genomes]
rs470098	0.89[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470101	0.80[CEU][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs470102	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470104	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55856549	0.89[EUR][1000 genomes]
rs56233401	0.95[EUR][1000 genomes]
rs56393679	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57686964	0.95[EUR][1000 genomes]
rs58050941	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58823697	0.95[EUR][1000 genomes]
rs7286519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288331	0.93[EUR][1000 genomes]
rs7289984	0.93[EUR][1000 genomes]
rs7292562	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880355	0.91[EUR][1000 genomes]
rs73880374	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880375	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880376	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880381	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880382	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880383	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880384	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880385	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880387	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880393	0.93[EUR][1000 genomes]
rs73880395	0.86[EUR][1000 genomes]
rs73882704	0.82[EUR][1000 genomes]
rs73882705	0.82[EUR][1000 genomes]
rs761322	0.87[EUR][1000 genomes]
rs761323	0.95[EUR][1000 genomes]
rs8141163	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs8141173	0.93[EUR][1000 genomes]
rs9306451	0.88[CEU][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306452	0.87[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs9620752	0.93[EUR][1000 genomes]
rs9620753	0.93[EUR][1000 genomes]
rs9620755	0.90[EUR][1000 genomes]
rs9620757	0.93[EUR][1000 genomes]
rs9620762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620766	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620767	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620768	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620769	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs9620770	1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.86[EUR][1000 genomes]
rs9620771	0.93[EUR][1000 genomes]
rs9625352	0.89[MEX][hapmap]
rs9625361	0.91[EUR][1000 genomes]
rs9625363	0.93[EUR][1000 genomes]
rs9625366	0.91[EUR][1000 genomes]
rs9625367	0.93[EUR][1000 genomes]
rs9625370	0.93[EUR][1000 genomes]
rs9625374	0.93[EUR][1000 genomes]
rs9625375	0.93[EUR][1000 genomes]
rs9625377	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625387	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625388	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625390	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625391	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625393	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625395	0.89[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625396	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625397	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625398	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625399	0.88[CEU][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625400	0.86[CEU][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625402	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625403	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625405	0.88[CEU][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs9625406	0.85[EUR][1000 genomes]
rs9625407	0.84[EUR][1000 genomes]
rs9625408	1.00[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs9625409	0.93[EUR][1000 genomes]
rs9625410	0.91[EUR][1000 genomes]
rs9625413	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9625415	0.93[EUR][1000 genomes]
rs9625416	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9625417	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs9625418	0.93[EUR][1000 genomes]
rs9625421	0.89[EUR][1000 genomes]
rs9625425	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9625427	0.84[EUR][1000 genomes]
rs9625430	0.86[EUR][1000 genomes]
rs9712839	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988893	0.82[EUR][1000 genomes]
rs9985213	0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
2	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
3	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr22:28386200-28405800	Strong transcription	Dnd41	blood
6	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
9	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
13	chr22:28392200-28405200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr22:28393400-28408800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:28394200-28405000	Weak transcription	Fetal Brain Male	brain
16	chr22:28394200-28405000	Weak transcription	NHDF-Ad	bronchial
17	chr22:28394800-28414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr22:28395200-28405000	Weak transcription	Brain Substantia Nigra	brain
20	chr22:28395200-28405200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr22:28395200-28409200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:28395400-28404600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr22:28395400-28406400	Weak transcription	Aorta	Aorta
24	chr22:28395400-28409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr22:28395600-28408200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
27	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
28	chr22:28396800-28407600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr22:28397200-28404200	Weak transcription	Colon Smooth Muscle	Colon
30	chr22:28397200-28405000	Weak transcription	Brain Hippocampus Middle	brain
31	chr22:28397200-28409400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr22:28397200-28423000	Weak transcription	HepG2	liver
33	chr22:28397400-28405000	Weak transcription	Brain Anterior Caudate	brain
34	chr22:28397400-28408800	Weak transcription	Brain Angular Gyrus	brain
35	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
36	chr22:28397600-28404600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:28397600-28405000	Weak transcription	Gastric	stomach
38	chr22:28398000-28405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:28398400-28405600	Weak transcription	Esophagus	oesophagus
40	chr22:28399400-28425800	Weak transcription	Liver	Liver
41	chr22:28399600-28409000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr22:28400600-28405200	Weak transcription	Fetal Intestine Large	intestine
43	chr22:28400800-28410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:28401600-28404600	Weak transcription	Ovary	ovary
45	chr22:28401600-28405000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:28401600-28405200	Weak transcription	Adipose Nuclei	Adipose
47	chr22:28401600-28405200	Weak transcription	Fetal Lung	lung
48	chr22:28401600-28409000	Strong transcription	Fetal Muscle Leg	muscle
49	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
50	chr22:28401800-28407800	Weak transcription	Lung	lung

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