Variant report

Variant	rs470101
Chromosome Location	chr22:28389453-28389454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28387405..28389960-chr22:28390673..28392531,2	K562	blood:
2	chr22:28386424..28391096-chr22:28391178..28396307,7	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28389112-28389493	ENSG00000235954
2	lnc-HSCB-1	chr22:28388916-28389523	ENSG00000235954
3	lnc-HSCB-1	chr22:28388457-28389523	ENSG00000235954
4	lnc-HSCB-1	chr22:28389112-28389523	ENSG00000235954
5	lnc-HSCB-1	chr22:28389112-28389514	NONHSAT084636

No data

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction
ENSG00000100154	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10154425	0.80[CEU][hapmap]
rs10483140	0.90[CEU][hapmap]
rs10483141	1.00[CHB][hapmap]
rs10483143	0.89[MEX][hapmap]
rs118840	0.90[CEU][hapmap];1.00[MEX][hapmap]
rs12166077	0.80[CEU][hapmap];0.89[MEX][hapmap]
rs12166389	0.90[CEU][hapmap]
rs12166740	0.89[MEX][hapmap];0.82[YRI][hapmap]
rs12167128	0.82[ASW][hapmap]
rs12168054	0.80[CEU][hapmap]
rs12168582	0.90[CEU][hapmap];1.00[MEX][hapmap]
rs12170161	0.90[MEX][hapmap]
rs12170953	0.80[CEU][hapmap]
rs12171104	0.90[CEU][hapmap]
rs135641	1.00[CHB][hapmap]
rs135642	1.00[CHB][hapmap]
rs135644	1.00[CHB][hapmap]
rs135645	1.00[CHB][hapmap]
rs135649	1.00[CHB][hapmap]
rs138636	0.90[CEU][hapmap];1.00[MEX][hapmap]
rs138637	0.90[CEU][hapmap]
rs138639	0.90[CEU][hapmap];1.00[MEX][hapmap]
rs138640	0.90[CEU][hapmap]
rs138642	0.90[CEU][hapmap];0.89[MEX][hapmap]
rs138645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138646	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs138648	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs138653	0.80[CEU][hapmap]
rs138656	0.80[CEU][hapmap]
rs138658	0.80[CEU][hapmap]
rs138660	0.80[CEU][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs138664	0.80[CEU][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs138665	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs138667	0.80[CEU][hapmap]
rs138671	0.80[CEU][hapmap]
rs138676	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs138679	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs138680	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569700	1.00[CHB][hapmap]
rs16985691	0.89[MEX][hapmap]
rs16985967	0.89[MEX][hapmap]
rs17483887	0.80[CEU][hapmap];0.89[MEX][hapmap]
rs17484337	0.80[CEU][hapmap]
rs2038287	1.00[CHB][hapmap]
rs2143420	1.00[CHB][hapmap]
rs2345011	1.00[CHB][hapmap]
rs470098	0.90[CEU][hapmap]
rs470102	0.80[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs470103	0.80[CEU][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs73880371	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8141163	0.90[CEU][hapmap]
rs8142920	0.89[MEX][hapmap]
rs9620762	0.80[CEU][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs9620764	0.80[CEU][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs9620768	0.89[MEX][hapmap];0.91[YRI][hapmap]
rs9625352	1.00[MEX][hapmap]
rs9625387	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs9625390	0.80[CEU][hapmap]
rs9625391	0.80[CEU][hapmap];0.89[MEX][hapmap]
rs9625395	0.91[YRI][hapmap]
rs9625408	0.80[CEU][hapmap]

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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28360800-28392400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
3	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
5	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
7	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
8	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
9	chr22:28377800-28391800	Strong transcription	Fetal Lung	lung
10	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
11	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr22:28380200-28390400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr22:28381600-28393800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr22:28382200-28394000	Weak transcription	Brain Substantia Nigra	brain
18	chr22:28382800-28391800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr22:28382800-28394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:28384000-28390600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr22:28384200-28390600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr22:28384200-28399400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr22:28384400-28392600	Strong transcription	Brain Germinal Matrix	brain
25	chr22:28384600-28397600	Strong transcription	Ovary	ovary
26	chr22:28384800-28401600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr22:28385000-28390400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr22:28385000-28393400	Weak transcription	HSMM	muscle
29	chr22:28385200-28390800	Weak transcription	Brain Hippocampus Middle	brain
30	chr22:28386000-28390000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr22:28386200-28405800	Strong transcription	Dnd41	blood
32	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr22:28386400-28389600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr22:28387200-28389600	Weak transcription	HUVEC	blood vessel
35	chr22:28387400-28390600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr22:28387400-28392400	Weak transcription	Osteobl	bone
37	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr22:28387600-28393800	Weak transcription	NHDF-Ad	bronchial
39	chr22:28387600-28394600	Weak transcription	HepG2	liver
40	chr22:28387600-28398200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
42	chr22:28387800-28389800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr22:28387800-28392000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:28387800-28392000	Strong transcription	Brain Anterior Caudate	brain
45	chr22:28387800-28392400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:28387800-28392400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr22:28387800-28395600	Strong transcription	Pancreas	Pancrea
48	chr22:28387800-28397400	Strong transcription	Placenta	Placenta
49	chr22:28387800-28399000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr22:28387800-28399200	Strong transcription	Fetal Muscle Leg	muscle

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