Variant report

Variant	rs6760959
Chromosome Location	chr2:55821501-55821502
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55818907..55824295-chr2:55841098..55846037,6	MCF-7	breast:
2	chr2:55820891..55824510-chr2:55834569..55837738,3	K562	blood:

Variant related genes	Relation type
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10172181	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10172506	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10173150	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10182131	0.83[AMR][1000 genomes]
rs10195281	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10200159	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203953	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204169	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10221888	0.84[YRI][hapmap]
rs10427222	0.86[YRI][hapmap]
rs1045920	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10496044	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10496049	0.90[YRI][hapmap]
rs11676573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900763	0.87[YRI][hapmap]
rs11902712	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12463766	0.82[AFR][1000 genomes]
rs12615063	1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs12616502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616982	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12622830	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12623625	0.83[AMR][1000 genomes]
rs12989898	0.97[YRI][hapmap];0.89[AFR][1000 genomes]
rs13028892	0.86[YRI][hapmap]
rs13382187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13383352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13399762	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13400946	0.83[AMR][1000 genomes]
rs13407344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13420929	0.83[AMR][1000 genomes]
rs13428382	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13428486	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430684	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17047094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17047119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867964	0.83[AMR][1000 genomes]
rs3748945	0.96[YRI][hapmap]
rs3748955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816489	0.86[YRI][hapmap]
rs4671248	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs4671250	0.84[AFR][1000 genomes]
rs6545507	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545508	1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6545509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545512	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6545513	1.00[CHB][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6712314	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6725101	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6736996	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6745430	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6745650	0.96[YRI][hapmap]
rs730884	0.83[AFR][1000 genomes]
rs736345	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs744514	0.97[YRI][hapmap];0.85[AFR][1000 genomes]
rs7558127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7567115	0.83[AMR][1000 genomes]
rs7574398	0.92[AFR][1000 genomes]
rs7574409	0.85[AFR][1000 genomes]
rs7575906	0.83[AMR][1000 genomes]
rs7582174	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586115	0.83[AMR][1000 genomes]
rs7586124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586366	0.83[AMR][1000 genomes]
rs7594212	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9309267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309268	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9636439	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9808054	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
6	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
9	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
10	chr2:55794400-55825200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:55794400-55829000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:55796800-55823800	Weak transcription	Thymus	Thymus
13	chr2:55796800-55825200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:55796800-55825600	Weak transcription	Pancreas	Pancrea
15	chr2:55796800-55829400	Weak transcription	Esophagus	oesophagus
16	chr2:55796800-55842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:55797000-55824200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:55797000-55828000	Weak transcription	Aorta	Aorta
19	chr2:55797000-55829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55797000-55829600	Weak transcription	Gastric	stomach
21	chr2:55803000-55838800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:55803200-55823800	Weak transcription	Lung	lung
23	chr2:55804000-55824000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:55804400-55825200	Weak transcription	K562	blood
25	chr2:55806600-55825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:55806800-55825200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:55807400-55823000	Weak transcription	Fetal Kidney	kidney
28	chr2:55808200-55824800	Weak transcription	Colonic Mucosa	Colon
29	chr2:55810600-55829600	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:55811400-55829400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:55811600-55825000	Weak transcription	Fetal Brain Female	brain
32	chr2:55812400-55823400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:55812600-55823000	Weak transcription	Fetal Lung	lung
34	chr2:55814200-55822400	Weak transcription	Primary B cells from cord blood	blood
35	chr2:55814200-55825200	Weak transcription	HUVEC	blood vessel
36	chr2:55814200-55825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:55814200-55829000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:55814200-55829400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:55814400-55824200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:55814400-55826000	Weak transcription	GM12878-XiMat	blood
41	chr2:55815000-55823200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:55815200-55825400	Weak transcription	Hela-S3	cervix
43	chr2:55815400-55823800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:55815600-55822400	Weak transcription	Fetal Stomach	stomach
45	chr2:55815800-55822200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:55815800-55822800	Weak transcription	Liver	Liver
47	chr2:55815800-55822800	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:55815800-55823000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:55816000-55823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:55816000-55823400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links