Variant report

Variant	rs10752947
Chromosome Location	chr1:185263628-185263629
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185256584..185258275-chr1:185263468..185265157,2	K562	blood:
2	chr1:185262982..185267023-chr1:185274757..185279030,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10174	0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798002	0.87[ASN][1000 genomes]
rs10798003	0.82[TSI][hapmap]
rs10798004	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs10911700	0.81[TSI][hapmap]
rs10911702	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10911704	0.89[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.80[ASN][1000 genomes]
rs12026391	0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12041704	0.84[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs1889976	0.82[TSI][hapmap]
rs2152707	0.84[ASN][1000 genomes]
rs2378909	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2378910	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs6685627	0.88[ASN][1000 genomes]
rs6687774	0.80[MEX][hapmap]
rs7123	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs726567	0.84[CHB][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs7545878	0.86[GIH][hapmap]
rs883753	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10752947	RNF2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185218800-185269400	Weak transcription	Pancreas	Pancrea
2	chr1:185235400-185265400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:185236600-185265600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:185239800-185263800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:185240000-185265800	Weak transcription	Fetal Lung	lung
6	chr1:185240200-185267200	Weak transcription	Gastric	stomach
7	chr1:185240400-185268800	Weak transcription	Aorta	Aorta
8	chr1:185240800-185273000	Weak transcription	Spleen	Spleen
9	chr1:185244800-185264800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:185245400-185268800	Weak transcription	Esophagus	oesophagus
11	chr1:185245800-185268400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:185245800-185273000	Weak transcription	Right Ventricle	heart
13	chr1:185246800-185265600	Weak transcription	NHLF	lung
14	chr1:185247600-185267800	Weak transcription	Fetal Stomach	stomach
15	chr1:185248200-185266800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:185248800-185265200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:185249200-185265800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:185250200-185264000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:185250200-185265400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:185250400-185265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:185250600-185263800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:185251200-185264400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:185251200-185265600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:185251200-185266400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:185252000-185266000	Weak transcription	Thymus	Thymus
26	chr1:185254000-185264000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:185254200-185265600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:185254400-185263800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:185254400-185266600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:185254400-185267800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:185254600-185266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:185255000-185268200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:185255200-185265600	Weak transcription	Psoas Muscle	Psoas
34	chr1:185257000-185266000	Weak transcription	Ovary	ovary
35	chr1:185258200-185266000	Weak transcription	Fetal Heart	heart
36	chr1:185258600-185265400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:185258600-185266800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr1:185258800-185265600	Weak transcription	Fetal Brain Male	brain
39	chr1:185260400-185263800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:185260600-185265200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:185260800-185264000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:185260800-185275200	Weak transcription	Small Intestine	intestine
43	chr1:185261000-185263800	Weak transcription	Hela-S3	cervix
44	chr1:185261200-185264000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:185261200-185264200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:185261200-185267800	Weak transcription	Fetal Intestine Small	intestine
47	chr1:185261400-185264200	Weak transcription	NHDF-Ad	bronchial
48	chr1:185261400-185278800	Strong transcription	HUVEC	blood vessel
49	chr1:185261600-185265200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:185261800-185264600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links