Variant report

Variant	rs10754051
Chromosome Location	chr1:193133527-193133528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:192878910..192881090-chr1:193133221..193136133,2	K562	blood:
2	chr1:193091553..193093359-chr1:193132877..193135445,2	K562	blood:
3	chr1:193130707..193133682-chr1:193139194..193140778,2	K562	blood:

Variant related genes	Relation type
ENSG00000134371	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10921309	1.00[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap]
rs10921327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1539725	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6428156	0.82[CHD][hapmap]
rs6661522	0.87[CHD][hapmap];0.95[JPT][hapmap]
rs6697079	0.81[CHD][hapmap]
rs6698182	0.81[JPT][hapmap]

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	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10754051	CDC73	cis	cerebellum	SCAN
rs10754051	B3GALT2	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193092600-193141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:193094800-193155000	Weak transcription	Aorta	Aorta
3	chr1:193101000-193140000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:193104200-193135000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:193106000-193140800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:193110000-193139600	Weak transcription	Esophagus	oesophagus
7	chr1:193110000-193149400	Weak transcription	Right Ventricle	heart
8	chr1:193110000-193155200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:193111600-193137600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:193115800-193142000	Weak transcription	Spleen	Spleen
11	chr1:193116600-193149400	Weak transcription	Brain Germinal Matrix	brain
12	chr1:193118000-193147800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:193119600-193137600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:193120200-193141600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:193120400-193150400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:193120600-193135800	Weak transcription	Psoas Muscle	Psoas
17	chr1:193120600-193142000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:193121000-193143800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:193121000-193155200	Weak transcription	Pancreas	Pancrea
20	chr1:193121600-193137400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:193122400-193142400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:193123200-193140000	Weak transcription	Ovary	ovary
23	chr1:193123200-193147400	Weak transcription	Fetal Brain Female	brain
24	chr1:193123200-193151600	Weak transcription	Fetal Kidney	kidney
25	chr1:193123200-193153600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:193123400-193133800	Weak transcription	HMEC	breast
27	chr1:193123400-193139000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:193123400-193140000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:193123400-193140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:193123400-193140000	Weak transcription	HSMMtube	muscle
31	chr1:193123400-193142000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:193123400-193143000	Weak transcription	Lung	lung
33	chr1:193123400-193147600	Weak transcription	Fetal Brain Male	brain
34	chr1:193123400-193155200	Weak transcription	Thymus	Thymus
35	chr1:193123600-193140000	Weak transcription	Fetal Lung	lung
36	chr1:193123600-193149600	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:193123800-193141600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:193123800-193141800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:193123800-193147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:193123800-193150400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:193123800-193153200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:193124000-193152000	Weak transcription	Liver	Liver
43	chr1:193124000-193153600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:193124000-193154200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:193124200-193135600	Weak transcription	GM12878-XiMat	blood
46	chr1:193124200-193139800	Weak transcription	Adipose Nuclei	Adipose
47	chr1:193124200-193150400	Weak transcription	NHDF-Ad	bronchial
48	chr1:193124800-193141400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:193125200-193152200	Weak transcription	A549	lung
50	chr1:193125400-193134400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links