Variant report

Variant	rs872580
Chromosome Location	chr2:95722909-95722910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:95722350-95724206	HepG2	liver:	n/a	chr2:95723515-95723530
2	BHLHE40	chr2:95722485-95723027	HepG2	liver:	n/a	n/a
3	MAX	chr2:95722380-95724021	HepG2	liver:	n/a	chr2:95723515-95723530
4	ARID3A	chr2:95722814-95722931	HepG2	liver:	n/a	n/a
5	CTCF	chr2:95722900-95723050	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:95717464..95720060-chr2:95721874..95723809,2	MCF-7	breast:
2	chr2:95717110..95719318-chr2:95721681..95723671,2	K562	blood:
3	chr2:95718104..95721350-chr2:95721478..95724713,4	K562	blood:
4	chr2:95722359..95726880-chr2:95740082..95744931,5	MCF-7	breast:
5	chr2:95720619..95723205-chr2:95727451..95729974,2	MCF-7	breast:
6	chr2:95722035..95723837-chr2:95724936..95726737,2	K562	blood:

Variant related genes	Relation type
ENSG00000231062	TF binding region
ENSG00000231062	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10172167	0.86[CEU][hapmap]
rs17119148	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs1875402	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1966272	0.80[EUR][1000 genomes]
rs2001254	0.84[EUR][1000 genomes]
rs2098768	0.80[EUR][1000 genomes]
rs2291991	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2320619	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2320620	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2320621	0.83[EUR][1000 genomes]
rs2320624	0.83[EUR][1000 genomes]
rs3105098	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3105099	0.89[ASW][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs3105100	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3105101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105102	0.82[EUR][1000 genomes]
rs3105104	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3105105	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112221	0.85[EUR][1000 genomes]
rs3112222	0.84[EUR][1000 genomes]
rs3112223	0.85[EUR][1000 genomes]
rs3112225	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3112228	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3112229	0.80[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs3112230	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112231	0.88[EUR][1000 genomes]
rs3112982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3112984	0.94[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112985	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112986	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112987	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112988	0.81[ASN][1000 genomes]
rs3112990	0.81[ASN][1000 genomes]
rs3112995	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs3112996	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs3112997	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes]
rs3113000	0.83[EUR][1000 genomes]
rs3113001	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3113002	1.00[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs4241315	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555374	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs4564804	0.86[CEU][hapmap]
rs4854241	0.90[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4854243	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4854244	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4854247	0.82[EUR][1000 genomes]
rs6708474	0.85[CEU][hapmap]
rs6719098	0.82[EUR][1000 genomes]
rs6723333	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6725821	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs7560571	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs7565772	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7582368	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7585473	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9324212	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs872580	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95706200-95723800	Weak transcription	Fetal Kidney	kidney
2	chr2:95709600-95724000	Weak transcription	Pancreas	Pancrea
3	chr2:95714400-95724400	Weak transcription	Gastric	stomach
4	chr2:95716200-95723000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:95718000-95723000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:95719400-95724000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:95719600-95723200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:95719800-95723200	Enhancers	Primary T cells from cord blood	blood
9	chr2:95719800-95723600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:95719800-95723600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:95720800-95723600	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:95721200-95723600	Enhancers	Brain Hippocampus Middle	brain
13	chr2:95721400-95723600	Enhancers	Brain Anterior Caudate	brain
14	chr2:95721400-95723600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr2:95721400-95723600	Enhancers	Brain Substantia Nigra	brain
16	chr2:95721600-95724000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr2:95721600-95729800	Enhancers	Fetal Thymus	thymus
18	chr2:95721800-95723800	Enhancers	Brain Angular Gyrus	brain
19	chr2:95721800-95725400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:95722000-95723200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:95722000-95723200	Enhancers	HSMM	muscle
22	chr2:95722000-95724000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:95722000-95726400	Weak transcription	Dnd41	blood
24	chr2:95722000-95726400	Weak transcription	GM12878-XiMat	blood
25	chr2:95722000-95726600	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr2:95722200-95723000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:95722200-95723200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:95722200-95723200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:95722200-95723200	Enhancers	NH-A	brain
30	chr2:95722200-95723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:95722200-95723400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr2:95722200-95723600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr2:95722200-95723600	Enhancers	HMEC	breast
34	chr2:95722200-95725000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:95722200-95725400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:95722400-95723800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:95722400-95723800	Enhancers	Brain Germinal Matrix	brain
38	chr2:95722400-95726800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:95722400-95726800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:95722400-95727200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:95722600-95723000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:95722600-95723000	Genic enhancers	Thymus	Thymus
43	chr2:95722600-95723800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:95722600-95723800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:95722600-95723800	Enhancers	Fetal Muscle Leg	muscle
46	chr2:95722600-95724000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr2:95722600-95726400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:95722600-95726600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:95722800-95723200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:95722800-95724400	Weak transcription	Esophagus	oesophagus

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