Variant report

Variant	rs12693454
Chromosome Location	chr2:187457588-187457589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187360313..187361827-chr2:187456108..187458564,2	K562	blood:
2	chr2:187349672..187352615-chr2:187454696..187458504,4	K562	blood:
3	chr2:187350319..187353074-chr2:187452754..187457832,8	K562	blood:
4	chr2:187349171..187351570-chr2:187457346..187459477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065548	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10171481	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10172499	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10804007	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13006571	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992898	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165656	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2197138	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2197787	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2370693	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2887827	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768778	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768780	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3845712	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3911084	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233788	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434190	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66630114	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6741369	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72903148	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7596996	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333287	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333288	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1014203	chr2:187413781-187477586	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv536083	chr2:187413781-187477586	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv2756507	chr2:187416494-187470494	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv2756956	chr2:187416599-187492742	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv818105	chr2:187423298-187481835	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv2753217	chr2:187424494-187470494	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187453600-187458800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:187453800-187458000	Active TSS	Right Ventricle	heart
3	chr2:187454200-187457600	Active TSS	HSMMtube	muscle
4	chr2:187455200-187457600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr2:187456000-187468400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:187456000-187470600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:187456000-187488200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr2:187456200-187458800	Weak transcription	Small Intestine	intestine
9	chr2:187456200-187459600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:187456200-187462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:187456200-187468000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:187456200-187469600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
14	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:187456400-187457800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:187456400-187458800	Weak transcription	Stomach Mucosa	stomach
17	chr2:187456400-187459200	Weak transcription	Psoas Muscle	Psoas
18	chr2:187456400-187462400	Weak transcription	Lung	lung
19	chr2:187456400-187466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:187456400-187466800	Weak transcription	Placenta	Placenta
21	chr2:187456400-187469600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:187456400-187469800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:187456400-187488200	Weak transcription	Fetal Thymus	thymus
24	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:187456600-187457600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:187456600-187457600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:187456600-187458000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:187456600-187458000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:187456600-187458600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:187456600-187458800	Weak transcription	Ovary	ovary
31	chr2:187456600-187459200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:187456600-187459800	Weak transcription	Fetal Lung	lung
33	chr2:187456600-187460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:187456600-187460000	Weak transcription	Fetal Kidney	kidney
35	chr2:187456600-187460800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:187456600-187461800	Weak transcription	Aorta	Aorta
37	chr2:187456600-187462200	Enhancers	Brain Cingulate Gyrus	brain
38	chr2:187456600-187464200	Weak transcription	Fetal Stomach	stomach
39	chr2:187456600-187467600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:187456600-187469400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:187456600-187469600	Weak transcription	Primary T cells from cord blood	blood
42	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
43	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:187456800-187458000	Flanking Active TSS	HUVEC	blood vessel
45	chr2:187456800-187468000	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:187456800-187468000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr2:187456800-187469200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
49	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:187457000-187457600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links