Variant report

Variant	rs138651
Chromosome Location	chr22:28395923-28395924
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28386424..28391096-chr22:28391178..28396307,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28395418-28397646	ENSG00000235954
2	lnc-HSCB-1	chr22:28395418-28395991	NONHSAT084643

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10154425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs10212007	0.84[EUR][1000 genomes]
rs10212036	0.86[EUR][1000 genomes]
rs10483140	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs10483142	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483143	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs118840	0.86[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12165651	0.93[EUR][1000 genomes]
rs12165797	0.93[EUR][1000 genomes]
rs12166023	0.86[CEU][hapmap];0.80[YRI][hapmap];0.93[EUR][1000 genomes]
rs12166077	1.00[CEU][hapmap];0.96[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	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166389	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs12166719	0.80[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166740	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12166912	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs12166938	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167320	0.93[EUR][1000 genomes]
rs12167829	0.93[EUR][1000 genomes]
rs12168054	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs12168180	0.86[CEU][hapmap];0.80[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168251	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168582	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs12169097	0.93[EUR][1000 genomes]
rs12169888	0.84[AFR][1000 genomes];0.93[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	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170953	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171104	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs138636	0.86[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138637	0.86[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138639	0.86[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138640	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138642	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138648	0.86[CEU][hapmap]
rs138653	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138654	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138655	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138656	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs138658	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138660	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[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138665	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138667	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138669	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138670	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs138671	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138676	0.86[CEU][hapmap]
rs138679	0.86[CEU][hapmap]
rs138680	0.86[CEU][hapmap]
rs16985763	0.93[EUR][1000 genomes]
rs16985967	0.89[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16985976	0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs16986037	0.86[CEU][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes]
rs16986077	0.86[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs16987005	0.86[CEU][hapmap];0.80[YRI][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[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17484337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143420	0.89[YRI][hapmap]
rs2745562	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28579300	0.82[EUR][1000 genomes]
rs4036493	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs470098	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470102	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470103	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470104	1.00[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	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58823697	0.95[EUR][1000 genomes]
rs7286519	0.97[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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880376	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880382	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880383	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880384	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880385	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73880387	0.84[AFR][1000 genomes];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	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs761323	0.95[EUR][1000 genomes]
rs8141163	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs8141173	0.93[EUR][1000 genomes]
rs9306451	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306452	0.85[CEU][hapmap];1.00[YRI][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[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620764	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620766	0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620767	0.80[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620768	0.86[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620769	0.86[CEU][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes]
rs9620770	0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs9620771	0.93[EUR][1000 genomes]
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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625390	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625391	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625393	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625395	0.86[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625396	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625397	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625398	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625399	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625400	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625402	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625403	0.80[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625405	0.85[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs9625406	0.85[EUR][1000 genomes]
rs9625407	0.84[EUR][1000 genomes]
rs9625408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs9625409	0.93[EUR][1000 genomes]
rs9625410	0.91[EUR][1000 genomes]
rs9625413	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs9625415	0.93[EUR][1000 genomes]
rs9625416	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs9625417	0.86[CEU][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs9625418	0.93[EUR][1000 genomes]
rs9625421	0.89[EUR][1000 genomes]
rs9625425	0.86[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:2 , 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
2	nsv522306	chr22:28378472-28402624	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
2	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
4	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
5	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
6	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
7	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr22:28384200-28399400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr22:28384600-28397600	Strong transcription	Ovary	ovary
14	chr22:28384800-28401600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr22:28386200-28405800	Strong transcription	Dnd41	blood
16	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr22:28387600-28398200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
20	chr22:28387800-28397400	Strong transcription	Placenta	Placenta
21	chr22:28387800-28399000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr22:28387800-28399200	Strong transcription	Fetal Muscle Leg	muscle
23	chr22:28388000-28397200	Strong transcription	Lung	lung
24	chr22:28388200-28396800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr22:28388400-28400600	Weak transcription	Thymus	Thymus
26	chr22:28388800-28399800	Weak transcription	HSMMtube	muscle
27	chr22:28389000-28397400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
32	chr22:28391200-28402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr22:28392200-28405200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr22:28392600-28398000	Strong transcription	Fetal Lung	lung
35	chr22:28393000-28398000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:28393400-28397600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:28393400-28398200	Strong transcription	Brain Germinal Matrix	brain
38	chr22:28393400-28408800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:28393600-28396000	Strong transcription	Primary T cells from cord blood	blood
40	chr22:28393600-28397200	Strong transcription	Brain Hippocampus Middle	brain
41	chr22:28393800-28396000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr22:28393800-28397200	Strong transcription	Colon Smooth Muscle	Colon
43	chr22:28394000-28397400	Strong transcription	NHLF	lung
44	chr22:28394000-28397600	Strong transcription	Right Ventricle	heart
45	chr22:28394000-28398200	Strong transcription	Adipose Nuclei	Adipose
46	chr22:28394200-28398000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:28394200-28400600	Weak transcription	HSMM	muscle
48	chr22:28394200-28401000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr22:28394200-28405000	Weak transcription	Fetal Brain Male	brain
50	chr22:28394200-28405000	Weak transcription	NHDF-Ad	bronchial

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