Variant report

Variant	rs6542923
Chromosome Location	chr2:100892516-100892517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100887684..100889414-chr2:100891922..100893717,2	K562	blood:
2	chr2:100889401..100893026-chr2:100904259..100909793,5	MCF-7	breast:
3	chr2:100891457..100894388-chr2:100906302..100910364,4	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10170878	1.00[JPT][hapmap]
rs10173499	1.00[JPT][hapmap]
rs10865039	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs12463633	1.00[JPT][hapmap]
rs12464505	1.00[JPT][hapmap]
rs12467008	1.00[JPT][hapmap]
rs12472141	1.00[JPT][hapmap]
rs13024601	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs13397337	1.00[JPT][hapmap]
rs2309815	1.00[JPT][hapmap]
rs2309817	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309818	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2309819	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2309820	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2309821	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309822	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309824	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309825	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309826	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2871341	1.00[JPT][hapmap]
rs4561689	0.86[ASN][1000 genomes]
rs4851281	1.00[JPT][hapmap]
rs4851282	1.00[JPT][hapmap]
rs4851283	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851284	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851287	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6542919	1.00[JPT][hapmap]
rs6542924	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6724490	1.00[JPT][hapmap]
rs6727712	1.00[JPT][hapmap]
rs6754867	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6755791	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7421891	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7559464	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7562372	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7582180	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs7588623	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7590008	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7601873	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7607170	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7609376	0.85[CEU][hapmap];1.00[JPT][hapmap]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100879400-100896200	Weak transcription	Spleen	Spleen
2	chr2:100879400-100900200	Weak transcription	Brain Substantia Nigra	brain
3	chr2:100880200-100898400	Weak transcription	A549	lung
4	chr2:100884200-100900200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:100884800-100897400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:100885600-100898200	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:100885600-100902000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:100887000-100900200	Weak transcription	Left Ventricle	heart
9	chr2:100887200-100898000	Weak transcription	Fetal Brain Female	brain
10	chr2:100887800-100895000	Weak transcription	K562	blood
11	chr2:100887800-100901800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:100888000-100898000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:100888200-100896000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:100888400-100894600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:100889400-100900200	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:100889600-100898200	Weak transcription	Fetal Brain Male	brain
17	chr2:100889600-100898400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:100890600-100900200	Weak transcription	Right Ventricle	heart
19	chr2:100891400-100900000	Weak transcription	Aorta	Aorta
20	chr2:100891600-100896000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:100891800-100900200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:100891800-100907600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:100892000-100894800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:100892000-100896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:100892000-100896200	Weak transcription	Ovary	ovary
26	chr2:100892000-100898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:100892000-100898600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:100892000-100902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:100892000-100904000	Weak transcription	Gastric	stomach
30	chr2:100892200-100893000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:100892200-100895400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:100892200-100898200	Weak transcription	Brain Germinal Matrix	brain
33	chr2:100892200-100900200	Weak transcription	Pancreas	Pancrea
34	chr2:100892200-100909800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:100892400-100900600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links