Variant report

Variant	rs138650
Chromosome Location	chr22:28393540-28393541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr22:28393507-28393885	GM12878	blood:	n/a	n/a
2	EBF1	chr22:28393450-28393953	GM12878	blood:	n/a	chr22:28393668-28393679
3	RUNX3	chr22:28393480-28393801	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28386557..28389416-chr22:28392270..28394268,2	MCF-7	breast:
2	chr22:28386424..28391096-chr22:28391178..28396307,7	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSCB-1	chr22:28393399-28393727	ENSG00000235954
2	lnc-HSCB-1	chr22:28393399-28393763	ENSG00000235954
3	lnc-HSCB-1	chr22:28393399-28393655	ENSG00000235954
4	lnc-HSCB-1	chr22:28393399-28393619	ENSG00000235954
5	lnc-HSCB-1	chr22:28393399-28393727	ENSG00000235954
6	lnc-HSCB-1	chr22:28393399-28393688	ENSG00000235954

No data

Variant related genes	Relation type
TTC28	TF binding region
TTC28-AS1	TF binding region
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028364	0.81[JPT][hapmap]
rs118839	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12171034	0.91[ASN][1000 genomes]
rs138631	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs138638	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs138675	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs138683	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs138685	0.87[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1548235	0.90[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2038158	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2092054	0.92[ASN][1000 genomes]
rs2267121	0.87[TSI][hapmap]
rs3747141	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4140571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs470100	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs470105	0.82[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752667	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762416	0.88[EUR][1000 genomes]
rs5762418	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6005671	0.89[CEU][hapmap];0.83[CHD][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs720621	0.80[CHD][hapmap];0.85[TSI][hapmap]
rs73425788	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs738451	0.81[ASW][hapmap];0.84[LWK][hapmap];0.87[TSI][hapmap]
rs7625	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs957601	0.88[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs138650	TTC28AS	cis	cerebellum	SCAN
rs138650	ZNF280A	cis	cerebellum	SCAN
rs138650	CHEK2	cis	cerebellum	SCAN
rs138650	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28369200-28398400	Weak transcription	Hela-S3	cervix
2	chr22:28369400-28394000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:28371800-28395000	Weak transcription	Small Intestine	intestine
4	chr22:28373600-28404000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:28373800-28398200	Strong transcription	Fetal Brain Female	brain
6	chr22:28373800-28404200	Strong transcription	Fetal Stomach	stomach
7	chr22:28373800-28405200	Strong transcription	Fetal Intestine Small	intestine
8	chr22:28377800-28398000	Strong transcription	Fetal Intestine Large	intestine
9	chr22:28377800-28398600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:28378000-28396600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:28379400-28399600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr22:28381600-28393800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr22:28382200-28394000	Weak transcription	Brain Substantia Nigra	brain
15	chr22:28382800-28394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:28384000-28405000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:28384200-28399400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr22:28384600-28397600	Strong transcription	Ovary	ovary
19	chr22:28384800-28401600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr22:28386200-28405800	Strong transcription	Dnd41	blood
21	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr22:28387400-28405200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr22:28387600-28393800	Weak transcription	NHDF-Ad	bronchial
24	chr22:28387600-28394600	Weak transcription	HepG2	liver
25	chr22:28387600-28398200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr22:28387600-28405000	Weak transcription	Fetal Kidney	kidney
27	chr22:28387800-28395600	Strong transcription	Pancreas	Pancrea
28	chr22:28387800-28397400	Strong transcription	Placenta	Placenta
29	chr22:28387800-28399000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr22:28387800-28399200	Strong transcription	Fetal Muscle Leg	muscle
31	chr22:28388000-28397200	Strong transcription	Lung	lung
32	chr22:28388200-28396800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr22:28388400-28393600	Weak transcription	Primary T cells from cord blood	blood
34	chr22:28388400-28393600	Weak transcription	Fetal Brain Male	brain
35	chr22:28388400-28395600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr22:28388400-28400600	Weak transcription	Thymus	Thymus
37	chr22:28388600-28394800	Weak transcription	Left Ventricle	heart
38	chr22:28388800-28394000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:28388800-28399800	Weak transcription	HSMMtube	muscle
40	chr22:28389000-28395800	Strong transcription	Brain Angular Gyrus	brain
41	chr22:28389000-28397400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:28389400-28394000	Weak transcription	Liver	Liver
45	chr22:28389600-28393800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
48	chr22:28391000-28395400	Strong transcription	Esophagus	oesophagus
49	chr22:28391200-28393800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:28391200-28402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links