Variant report

Variant	rs12131933
Chromosome Location	chr1:227501984-227501985
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227500962..227504758-chr1:227504964..227507747,3	MCF-7	breast:
2	chr1:227490028..227493033-chr1:227499168..227502183,4	K562	blood:
3	chr1:227491263..227493925-chr1:227500068..227502093,2	MCF-7	breast:
4	chr1:227500261..227502142-chr1:227623311..227626021,2	K562	blood:
5	chr1:227487011..227489287-chr1:227501111..227503917,2	MCF-7	breast:
6	chr1:227500332..227503244-chr1:227542452..227546426,3	K562	blood:

Variant related genes	Relation type
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10916112	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916113	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916116	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916125	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11576239	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11584325	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11585910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12119153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12119448	0.84[AFR][1000 genomes]
rs12123597	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12128174	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12131061	0.92[AMR][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12133230	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133633	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12138092	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12138364	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12138383	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138664	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12144205	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12746316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747807	0.84[AFR][1000 genomes]
rs12754677	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12755770	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1513607	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1513613	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17613235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2063661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28648445	1.00[AMR][1000 genomes]
rs34113967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34702208	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34897490	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35160496	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35952573	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4308948	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61834323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834590	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834625	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61834626	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6660168	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6675408	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675572	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6678714	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512871	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7518813	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539662	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7543419	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7548118	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227469200-227502600	Weak transcription	HSMM	muscle
2	chr1:227475000-227502000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:227487000-227502000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:227487600-227502400	Weak transcription	Osteobl	bone
5	chr1:227490200-227503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:227492600-227503400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:227495000-227503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:227496200-227502000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:227496200-227504800	Weak transcription	Gastric	stomach
10	chr1:227496400-227502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:227496800-227502000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:227497200-227502600	Weak transcription	Fetal Intestine Large	intestine
13	chr1:227497600-227502000	Weak transcription	Liver	Liver
14	chr1:227498200-227502000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227498200-227503000	Weak transcription	Brain Germinal Matrix	brain
16	chr1:227498200-227503200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:227498400-227502000	Weak transcription	HepG2	liver
18	chr1:227499200-227502400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:227499400-227503800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:227499600-227502000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:227500000-227502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:227500600-227502000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:227500600-227502000	Weak transcription	Fetal Brain Male	brain
24	chr1:227500600-227502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:227500600-227502200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:227500600-227503200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:227500600-227503200	Weak transcription	Placenta	Placenta
28	chr1:227500600-227503200	Weak transcription	Right Ventricle	heart
29	chr1:227500600-227503400	Weak transcription	Ovary	ovary
30	chr1:227500600-227503600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:227500600-227504800	Weak transcription	Lung	lung
32	chr1:227500800-227502000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:227500800-227502000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:227500800-227502000	Weak transcription	Psoas Muscle	Psoas
35	chr1:227500800-227502200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:227500800-227502200	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:227500800-227503200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:227500800-227503600	Weak transcription	Left Ventricle	heart
39	chr1:227500800-227504600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:227500800-227504600	Weak transcription	Pancreas	Pancrea
41	chr1:227500800-227506600	Active TSS	K562	blood
42	chr1:227501000-227502000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:227501200-227502000	Weak transcription	Brain Angular Gyrus	brain
44	chr1:227501200-227502000	Weak transcription	Brain Substantia Nigra	brain
45	chr1:227501200-227502000	Flanking Active TSS	HUVEC	blood vessel
46	chr1:227501200-227502200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:227501200-227502600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:227501200-227503200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:227501400-227502000	Weak transcription	Hela-S3	cervix
50	chr1:227501400-227502800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links