Variant report

Variant	rs7559651
Chromosome Location	chr2:54208938-54208939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54196641..54201530-chr2:54208327..54212751,6	K562	blood:
2	chr2:54197131..54199961-chr2:54207547..54210724,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1001296	1.00[CHB][hapmap]
rs10180492	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10181332	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10188834	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10190353	1.00[AMR][1000 genomes]
rs10199041	1.00[CHB][hapmap]
rs10199444	1.00[ASN][1000 genomes]
rs10199995	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207892	1.00[CHB][hapmap]
rs10208649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496027	0.90[YRI][hapmap]
rs1049894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11125517	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11125521	1.00[CHB][hapmap]
rs11884327	1.00[CHB][hapmap]
rs11884857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11886024	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886366	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11887593	1.00[AMR][1000 genomes]
rs11889527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11890472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891000	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891079	1.00[CHB][hapmap]
rs11892759	1.00[ASN][1000 genomes]
rs11894028	1.00[ASN][1000 genomes]
rs11896279	1.00[CHB][hapmap]
rs11904365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13387291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13389673	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390377	1.00[CHB][hapmap]
rs13395751	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13401491	1.00[AMR][1000 genomes]
rs13401719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402778	1.00[ASN][1000 genomes]
rs13414565	1.00[CHB][hapmap]
rs13417051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425337	1.00[CHB][hapmap]
rs13432387	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404994	1.00[ASN][1000 genomes]
rs17039541	0.90[YRI][hapmap]
rs17045242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17045513	1.00[CHB][hapmap]
rs1872328	1.00[CHB][hapmap]
rs2090182	1.00[CHB][hapmap]
rs2112120	1.00[AMR][1000 genomes]
rs2161083	1.00[AMR][1000 genomes]
rs2177791	1.00[ASN][1000 genomes]
rs2177792	1.00[ASN][1000 genomes]
rs2287347	0.80[CEU][hapmap]
rs28391754	1.00[ASN][1000 genomes]
rs28571698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41536750	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4553857	1.00[CHB][hapmap]
rs58920915	1.00[AMR][1000 genomes]
rs60769690	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60776154	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6545367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6545368	0.80[CEU][hapmap]
rs6545369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6545372	1.00[ASN][1000 genomes]
rs6545382	0.94[AMR][1000 genomes]
rs6712561	1.00[ASN][1000 genomes]
rs6715161	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6719990	1.00[AMR][1000 genomes]
rs6723722	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730494	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6731217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731911	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740063	1.00[ASN][1000 genomes]
rs6745729	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748686	1.00[AMR][1000 genomes]
rs6751340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6759437	1.00[ASN][1000 genomes]
rs6761648	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902931	1.00[ASN][1000 genomes]
rs72904915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72906704	0.94[AMR][1000 genomes]
rs72906711	1.00[AMR][1000 genomes]
rs72906714	1.00[AMR][1000 genomes]
rs73937421	1.00[ASN][1000 genomes]
rs7556936	0.94[AMR][1000 genomes]
rs7560575	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565152	1.00[ASN][1000 genomes]
rs7567225	1.00[ASN][1000 genomes]
rs7567556	1.00[CHB][hapmap]
rs7567614	1.00[CHB][hapmap]
rs7583508	0.94[AMR][1000 genomes]
rs7588134	0.87[AMR][1000 genomes]
rs7588319	1.00[AMR][1000 genomes]
rs7594327	1.00[ASN][1000 genomes]
rs7594400	1.00[CHB][hapmap]
rs7599335	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604464	1.00[CHB][hapmap]
rs7608085	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7608989	1.00[ASN][1000 genomes]
rs9309251	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9678301	0.88[AMR][1000 genomes];0.89[EUR][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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
3	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
4	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
8	chr2:54199200-54209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:54199200-54210600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:54199200-54213800	Weak transcription	Psoas Muscle	Psoas
11	chr2:54199200-54213800	Weak transcription	Small Intestine	intestine
12	chr2:54199200-54214200	Weak transcription	Colonic Mucosa	Colon
13	chr2:54199200-54214200	Weak transcription	Fetal Heart	heart
14	chr2:54199200-54214200	Weak transcription	Fetal Kidney	kidney
15	chr2:54199200-54214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:54199200-54214200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:54199200-54214200	Weak transcription	NH-A	brain
18	chr2:54199200-54214400	Weak transcription	A549	lung
19	chr2:54199200-54214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:54199400-54209600	Weak transcription	HSMM	muscle
21	chr2:54200000-54214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:54200200-54211400	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:54200200-54212800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:54200200-54216600	Weak transcription	Right Ventricle	heart
25	chr2:54200400-54209800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:54200400-54218400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:54201200-54209000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr2:54201200-54209600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:54201400-54209000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:54201400-54209000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:54201400-54209000	Strong transcription	Fetal Intestine Large	intestine
32	chr2:54201400-54211400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:54201400-54211400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:54201800-54211600	Strong transcription	Primary T cells from cord blood	blood
35	chr2:54202200-54212600	Weak transcription	HepG2	liver
36	chr2:54202600-54211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:54202600-54214200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:54202600-54214400	Weak transcription	NHDF-Ad	bronchial
39	chr2:54202800-54210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:54202800-54214800	Weak transcription	NHLF	lung
41	chr2:54202800-54215800	Weak transcription	NHEK	skin
42	chr2:54203200-54214200	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:54203600-54214800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:54203800-54210400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:54203800-54211600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:54203800-54214200	Weak transcription	Brain Anterior Caudate	brain
47	chr2:54204000-54209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:54204000-54210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:54204400-54209400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:54204400-54226400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links