Variant report

Variant	rs12401293
Chromosome Location	chr1:185115815-185115816
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185113029..185115978-chr1:185116966..185118773,2	K562	blood:
2	chr1:185114068..185116270-chr1:185124385..185126877,5	MCF-7	breast:
3	chr1:185114176..185116855-chr1:185120494..185122664,2	K562	blood:
4	chr1:185113319..185116352-chr1:185124187..185127216,4	MCF-7	breast:
5	chr1:185115388..185115967-chr12:81272400..81273262,2	MCF-7	breast:
6	chr1:185112895..185116881-chr1:185123287..185126781,5	K562	blood:

Variant related genes	Relation type
ENSG00000121486	Chromatin interaction
ENSG00000116668	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1008502	0.80[EUR][1000 genomes]
rs1046592	0.85[EUR][1000 genomes]
rs10489581	0.97[EUR][1000 genomes]
rs10797997	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10797998	0.93[EUR][1000 genomes]
rs10911676	0.85[EUR][1000 genomes]
rs10911682	0.93[EUR][1000 genomes]
rs10911686	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022419	0.97[EUR][1000 genomes]
rs12023744	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12025995	0.97[EUR][1000 genomes]
rs12026000	0.97[EUR][1000 genomes]
rs12027607	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12028809	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12030778	0.97[EUR][1000 genomes]
rs12030967	0.90[EUR][1000 genomes]
rs12031837	0.97[EUR][1000 genomes]
rs12035073	0.97[EUR][1000 genomes]
rs12035433	0.97[EUR][1000 genomes]
rs12037466	0.90[EUR][1000 genomes]
rs12037692	0.97[EUR][1000 genomes]
rs12039541	0.90[EUR][1000 genomes]
rs12040650	0.86[AMR][1000 genomes]
rs12041374	0.97[EUR][1000 genomes]
rs12043427	0.97[EUR][1000 genomes]
rs12043495	0.97[EUR][1000 genomes]
rs12043561	0.97[EUR][1000 genomes]
rs12043617	0.85[EUR][1000 genomes]
rs12044161	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12044997	0.90[EUR][1000 genomes]
rs12045772	0.90[EUR][1000 genomes]
rs12046095	0.97[EUR][1000 genomes]
rs12046202	0.90[EUR][1000 genomes]
rs12046801	0.85[EUR][1000 genomes]
rs12049293	0.80[EUR][1000 genomes]
rs12064938	0.82[AMR][1000 genomes]
rs12086086	0.93[EUR][1000 genomes]
rs12094983	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12404644	0.87[EUR][1000 genomes]
rs12408279	0.85[EUR][1000 genomes]
rs12408500	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12409926	0.85[EUR][1000 genomes]
rs1407554	0.97[EUR][1000 genomes]
rs1544052	0.93[EUR][1000 genomes]
rs16865296	0.90[EUR][1000 genomes]
rs2273881	0.93[EUR][1000 genomes]
rs3766720	0.85[EUR][1000 genomes]
rs3766723	0.80[EUR][1000 genomes]
rs3806243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41264588	0.93[EUR][1000 genomes]
rs41264590	0.97[EUR][1000 genomes]
rs56107433	0.97[EUR][1000 genomes]
rs61125463	0.97[EUR][1000 genomes]
rs61495015	0.97[EUR][1000 genomes]
rs72724103	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72724108	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72739677	0.86[AMR][1000 genomes]
rs72741807	0.97[EUR][1000 genomes]
rs72741808	0.97[EUR][1000 genomes]
rs72741816	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72741817	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72741819	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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	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	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv872588	chr1:185081903-185117688	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548397	chr1:185104842-185123630	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
4	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
5	chr1:185085000-185121400	Weak transcription	NHEK	skin
6	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:185086000-185120200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:185087000-185125000	Weak transcription	Gastric	stomach
9	chr1:185087600-185117000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:185088200-185120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:185089400-185124400	Weak transcription	Colonic Mucosa	Colon
12	chr1:185089600-185121400	Weak transcription	Stomach Mucosa	stomach
13	chr1:185091200-185121400	Weak transcription	Fetal Heart	heart
14	chr1:185093800-185117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:185094200-185116600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:185094200-185118400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:185096600-185121400	Weak transcription	Hela-S3	cervix
18	chr1:185101000-185121000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
20	chr1:185101800-185120200	Strong transcription	Adipose Nuclei	Adipose
21	chr1:185101800-185120800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:185102000-185120800	Strong transcription	Placenta	Placenta
23	chr1:185102400-185120600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:185102400-185121400	Weak transcription	HMEC	breast
25	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
26	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
27	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine
28	chr1:185102800-185117400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:185102800-185121200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:185102800-185125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:185103000-185116600	Weak transcription	Fetal Brain Female	brain
32	chr1:185103000-185121400	Weak transcription	Aorta	Aorta
33	chr1:185103000-185124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:185103200-185117400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:185103200-185121000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:185103200-185121000	Weak transcription	HSMMtube	muscle
37	chr1:185103400-185123600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:185103600-185123800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:185103600-185124400	Weak transcription	Brain Substantia Nigra	brain
40	chr1:185104200-185123000	Weak transcription	HepG2	liver
41	chr1:185104600-185116600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:185104600-185125000	Weak transcription	Pancreas	Pancrea
43	chr1:185104800-185116600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:185105200-185120400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:185105600-185118400	Weak transcription	Thymus	Thymus
46	chr1:185105600-185125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:185105600-185125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:185105600-185125200	Weak transcription	Lung	lung
49	chr1:185106000-185124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:185106200-185123400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links