Variant report

Variant	rs7594497
Chromosome Location	chr2:55872538-55872539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55867632..55869380-chr2:55872094..55873711,2	K562	blood:
2	chr2:55842502..55844882-chr2:55870584..55873430,2	MCF-7	breast:
3	chr2:55844652..55846516-chr2:55872491..55875236,2	MCF-7	breast:
4	chr2:55872045..55873893-chr2:55874188..55876944,2	K562	blood:

Variant related genes	Relation type
ENSG00000138035	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10172181	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10172506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10173150	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10182131	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10194634	0.89[AMR][1000 genomes]
rs10195281	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10200159	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10203953	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10204169	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208774	0.83[YRI][hapmap]
rs10221888	0.90[YRI][hapmap]
rs10427222	0.93[YRI][hapmap]
rs1045920	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11676573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs11900763	0.93[YRI][hapmap]
rs11902712	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12615063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12616502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs12616982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12622830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623625	0.94[AMR][1000 genomes]
rs12989898	0.83[YRI][hapmap]
rs13028892	0.93[YRI][hapmap]
rs13382187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13384322	0.83[YRI][hapmap]
rs13399762	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13400946	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13403782	0.81[AFR][1000 genomes]
rs13407344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13420929	0.94[AMR][1000 genomes]
rs13428382	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13428486	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13430684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17047094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17047119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867964	0.94[AMR][1000 genomes]
rs3748945	0.83[YRI][hapmap]
rs3748955	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3816489	0.93[YRI][hapmap]
rs4671248	0.93[YRI][hapmap]
rs6545507	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545508	0.80[ASW][hapmap];1.00[CHD][hapmap];0.96[YRI][hapmap]
rs6545509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs6545510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545512	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545513	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705295	0.89[AMR][1000 genomes]
rs6712314	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6716100	0.86[YRI][hapmap]
rs6717574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6725101	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6736996	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6739788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745650	0.82[YRI][hapmap]
rs6760959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs736345	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs744514	0.82[YRI][hapmap]
rs7558127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567115	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7575906	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7582174	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7584120	0.80[YRI][hapmap];0.89[AFR][1000 genomes]
rs7586115	0.94[AMR][1000 genomes]
rs7586124	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586366	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7594212	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9309267	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309268	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9636439	0.93[YRI][hapmap]

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	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	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
4	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
5	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
6	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55848000-55872600	Weak transcription	Small Intestine	intestine
5	chr2:55849200-55873200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:55857000-55873800	Strong transcription	Fetal Thymus	thymus
9	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
10	chr2:55858800-55873400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:55858800-55877200	Strong transcription	Dnd41	blood
13	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:55859200-55874000	Weak transcription	Pancreas	Pancrea
17	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:55859800-55873200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:55859800-55873600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
22	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:55862000-55873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:55862000-55874800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
27	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:55862200-55873800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:55862200-55874000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:55862200-55874400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:55862200-55874800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:55863400-55875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:55864400-55919600	Weak transcription	NHLF	lung
37	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:55864800-55874800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:55864800-55879200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr2:55865000-55880400	Weak transcription	HMEC	breast
42	chr2:55865600-55873400	Strong transcription	Osteobl	bone
43	chr2:55866200-55873800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:55866200-55882400	Weak transcription	Ovary	ovary
45	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:55866800-55875000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:55867200-55875000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr2:55868000-55879200	Weak transcription	NH-A	brain
49	chr2:55868600-55873600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55868600-55874600	Strong transcription	Primary B cells from peripheral blood	blood

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