Variant report

Variant	rs3112996
Chromosome Location	chr2:95812372-95812373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95812124..95814661-chr3:183395640..183398578,2	MCF-7	breast:
2	chr2:95808395..95810463-chr2:95811272..95813300,2	MCF-7	breast:
3	chr2:95810413..95812459-chr2:95813819..95815894,2	K562	blood:

Variant related genes	Relation type
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10172167	0.81[CEU][hapmap]
rs10195614	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1104775	0.85[EUR][1000 genomes]
rs11164122	0.86[CEU][hapmap]
rs11897976	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs12992066	0.83[EUR][1000 genomes]
rs1559483	0.86[CEU][hapmap]
rs17119148	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1966272	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2001254	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010533	0.88[EUR][1000 genomes]
rs2042477	0.90[CEU][hapmap]
rs2098768	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2291991	0.84[EUR][1000 genomes]
rs2320339	0.86[EUR][1000 genomes]
rs2320619	0.86[EUR][1000 genomes]
rs2320620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2320621	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2320624	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105098	0.80[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3105099	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3105100	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3105101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3105102	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105105	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112221	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112222	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112223	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112228	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112229	0.85[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112231	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112982	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3112983	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3112984	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs3112985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs3112986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs3112987	0.88[EUR][1000 genomes]
rs3112990	0.82[ASN][1000 genomes]
rs3112995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112999	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3113000	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113001	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113002	1.00[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs3755520	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755521	0.81[CEU][hapmap]
rs3755523	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755525	0.86[CEU][hapmap]
rs3772041	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772042	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772043	0.86[CEU][hapmap]
rs3772044	0.95[CEU][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3821341	0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4241315	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4555374	0.81[CEU][hapmap]
rs4564804	0.81[CEU][hapmap]
rs4854241	0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs4854243	0.88[EUR][1000 genomes]
rs4854244	0.86[EUR][1000 genomes]
rs4854247	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4854249	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6577012	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6577013	0.86[CEU][hapmap];0.94[TSI][hapmap]
rs6708474	0.80[CEU][hapmap]
rs6715813	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6719098	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6723333	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6725821	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap]
rs6750542	0.90[CEU][hapmap]
rs7565772	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7574862	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7580685	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7582368	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs7585473	0.88[EUR][1000 genomes]
rs7585914	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs7586229	0.84[EUR][1000 genomes]
rs7594144	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs870393	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs872580	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]
rs889851	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889852	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889853	0.86[CEU][hapmap]
rs918811	0.90[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs9324212	0.81[CEU][hapmap]
rs9678800	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs9989786	0.85[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][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	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
2	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
3	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
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3112996	KCNIP3	cis	cerebellum	SCAN
rs3112996	ZNF514	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95803000-95821600	ZNF genes & repeats	Fetal Brain Female	brain
2	chr2:95803400-95821400	ZNF genes & repeats	Brain Germinal Matrix	brain
3	chr2:95803600-95822600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr2:95807600-95819200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
5	chr2:95807800-95821200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr2:95807800-95823200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:95808000-95821600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr2:95808000-95821600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
9	chr2:95808000-95823200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:95808200-95819000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
11	chr2:95808200-95821200	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr2:95808200-95821400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:95808200-95821400	ZNF genes & repeats	Fetal Lung	lung
14	chr2:95808200-95822000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:95808200-95822200	ZNF genes & repeats	Fetal Muscle Leg	muscle
16	chr2:95808200-95823000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr2:95808200-95823400	ZNF genes & repeats	Liver	Liver
18	chr2:95808400-95813000	ZNF genes & repeats	Ovary	ovary
19	chr2:95808400-95813000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
20	chr2:95808400-95819000	ZNF genes & repeats	Brain Substantia Nigra	brain
21	chr2:95808400-95820200	ZNF genes & repeats	Brain Hippocampus Middle	brain
22	chr2:95808400-95823800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:95808600-95812800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr2:95808600-95820200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
25	chr2:95809000-95813200	Weak transcription	Fetal Heart	heart
26	chr2:95809400-95823000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:95809400-95824600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:95809600-95813000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:95809600-95813000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr2:95809600-95820200	ZNF genes & repeats	Left Ventricle	heart
31	chr2:95809600-95823600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:95809600-95823600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:95809600-95823800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr2:95809800-95812800	ZNF genes & repeats	Aorta	Aorta
35	chr2:95809800-95818200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
36	chr2:95809800-95819200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:95809800-95820000	ZNF genes & repeats	Psoas Muscle	Psoas
38	chr2:95809800-95820200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
39	chr2:95809800-95820400	ZNF genes & repeats	Brain Anterior Caudate	brain
40	chr2:95809800-95823600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:95810000-95813000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
42	chr2:95810000-95819000	ZNF genes & repeats	Brain Angular Gyrus	brain
43	chr2:95810000-95820000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:95810000-95822800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr2:95810000-95824400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:95810200-95814200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:95810600-95812600	Weak transcription	Right Ventricle	heart
48	chr2:95811000-95814800	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr2:95811200-95813000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:95811200-95813200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links