Variant report

Variant	rs4426625
Chromosome Location	chr3:98504865-98504866
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98504178..98506190-chr3:98512483..98514423,2	MCF-7	breast:
2	chr3:98502998..98505782-chr3:98508615..98511357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064225	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1062196	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12107050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12330170	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13060012	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs14310	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440150	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1440151	0.84[JPT][hapmap];0.82[AMR][1000 genomes]
rs1440152	0.81[JPT][hapmap]
rs17270593	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1837500	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1866677	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866678	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866679	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875086	0.82[EUR][1000 genomes]
rs1967009	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2028393	0.84[EUR][1000 genomes]
rs2062059	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2119187	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2119188	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2262597	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334230	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs2439213	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439214	0.81[ASN][1000 genomes]
rs2439215	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439217	0.82[ASN][1000 genomes]
rs2439218	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439222	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2439223	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[EUR][1000 genomes]
rs2439225	0.83[EUR][1000 genomes]
rs2439228	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439229	0.87[ASN][1000 genomes]
rs2439231	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439236	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454673	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2454676	0.82[ASN][1000 genomes]
rs2454677	0.83[ASN][1000 genomes]
rs2454678	0.82[ASN][1000 genomes]
rs2454682	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs2454685	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2470857	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2470859	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2470861	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2470864	0.82[ASN][1000 genomes]
rs2470865	0.81[ASN][1000 genomes]
rs2470867	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2470869	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470879	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470881	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[EUR][1000 genomes]
rs2470885	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs28802000	0.93[ASN][1000 genomes]
rs2919234	0.83[ASN][1000 genomes]
rs2919236	0.87[ASN][1000 genomes]
rs34234373	0.93[ASN][1000 genomes]
rs34558202	0.93[ASN][1000 genomes]
rs3755574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3772098	0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs3772099	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs3772101	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3772102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3821359	0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs4425200	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];1.00[ASN][1000 genomes]
rs4425201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4426626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4494869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62278486	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6782630	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785935	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6788418	0.93[ASN][1000 genomes]
rs6788689	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790650	0.89[ASN][1000 genomes]
rs6804850	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808116	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs704585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7431448	0.82[AMR][1000 genomes]
rs7611929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7612036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7616275	0.93[ASN][1000 genomes]
rs828609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs844160	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs9289683	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9811305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9811449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811860	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814819	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815226	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];0.98[ASN][1000 genomes]
rs9823430	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843214	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9845558	0.93[ASN][1000 genomes]
rs9855175	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9860216	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9860264	0.81[EUR][1000 genomes]
rs9866570	0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs9867586	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9872152	0.82[AMR][1000 genomes]
rs9873932	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9878392	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9881519	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9883516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999147	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];1.00[ASN][1000 genomes]

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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:98494600-98506000	Enhancers	Aorta	Aorta
12	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
13	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
14	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
15	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
16	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:98499800-98514800	Weak transcription	Dnd41	blood
23	chr3:98500200-98506000	Enhancers	HMEC	breast
24	chr3:98500800-98505600	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:98501000-98506600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:98501000-98507400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:98501200-98513400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:98501400-98505800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:98501400-98506000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:98501400-98506000	Enhancers	NH-A	brain
31	chr3:98502000-98506000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:98502200-98505000	Enhancers	HepG2	liver
33	chr3:98502200-98506200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:98502200-98506600	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
36	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:98502600-98505800	Weak transcription	Fetal Intestine Large	intestine
39	chr3:98502600-98513400	Weak transcription	Fetal Stomach	stomach
40	chr3:98502800-98505200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:98502800-98505400	Strong transcription	Fetal Thymus	thymus
42	chr3:98503000-98505200	Enhancers	Adipose Nuclei	Adipose
43	chr3:98503000-98505200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:98503000-98505800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:98503000-98506400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr3:98503000-98508000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr3:98503000-98509200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:98503200-98505200	Weak transcription	Lung	lung
49	chr3:98503200-98505600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:98503200-98505600	Enhancers	NHDF-Ad	bronchial

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