Variant report

Variant	rs742253
Chromosome Location	chr1:209759045-209759046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209757079..209759138-chr1:209762314..209763873,2	MCF-7	breast:
2	chr1:209755400..209758215-chr1:209758415..209761254,2	K562	blood:
3	chr1:209754618..209756587-chr1:209758907..209761295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008118	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489339	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs12084657	0.91[EUR][1000 genomes]
rs17014744	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014768	0.94[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014769	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17014820	0.84[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014822	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014823	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17014830	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17014866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs17388107	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2067744	0.91[EUR][1000 genomes]
rs55688212	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55709381	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55967608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56025154	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56165413	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58987909	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60686175	0.91[EUR][1000 genomes]
rs61819949	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822168	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61822169	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822171	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822172	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6540543	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6663545	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6669549	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6698127	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7512091	0.84[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs7516885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536585	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs880782	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs880783	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs742253	TMCC2	cis	parietal	SCAN
rs742253	RCOR3	cis	cerebellum	SCAN
rs742253	PIGR	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209756800-209759200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr1:209756800-209759400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:209756800-209759600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:209757000-209759400	Active TSS	Brain Angular Gyrus	brain
5	chr1:209757000-209760000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:209757200-209759800	Enhancers	Fetal Heart	heart
7	chr1:209757800-209759600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:209757800-209759800	Bivalent Enhancer	Fetal Stomach	stomach
9	chr1:209758000-209760000	Enhancers	Fetal Kidney	kidney
10	chr1:209758200-209759600	Enhancers	Ovary	ovary
11	chr1:209758200-209763200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:209758400-209759200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
13	chr1:209758600-209759200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:209758600-209759200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr1:209758600-209759400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr1:209758600-209759400	Bivalent Enhancer	Fetal Intestine Small	intestine
17	chr1:209758600-209759400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
18	chr1:209758600-209759400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
19	chr1:209758600-209759600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:209758600-209759600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:209758600-209759600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
22	chr1:209758600-209759600	Enhancers	Esophagus	oesophagus
23	chr1:209758600-209759600	Enhancers	Psoas Muscle	Psoas
24	chr1:209758600-209759600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
25	chr1:209758800-209759200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr1:209758800-209759200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:209758800-209759200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
28	chr1:209758800-209759400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:209758800-209759400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:209758800-209759400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr1:209758800-209759400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:209758800-209759400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:209758800-209759400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:209758800-209759400	Enhancers	Adipose Nuclei	Adipose
35	chr1:209758800-209759400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr1:209758800-209759400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:209758800-209759400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr1:209758800-209759400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr1:209758800-209759400	Enhancers	Spleen	Spleen
40	chr1:209758800-209759400	Bivalent/Poised TSS	A549	lung
41	chr1:209758800-209759600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:209758800-209759600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr1:209758800-209759600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:209758800-209759600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr1:209758800-209759600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
46	chr1:209758800-209759600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:209758800-209759600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:209758800-209759600	Bivalent Enhancer	Liver	Liver
49	chr1:209758800-209759600	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:209758800-209759600	Flanking Active TSS	Fetal Brain Male	brain

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