Variant report

Variant	rs17278047
Chromosome Location	chr3:98598944-98598945
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98597641..98599720-chr3:98602345..98604464,2	K562	blood:
2	chr3:98596084..98598965-chr3:98619062..98620700,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10433438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511169	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511171	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935542	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935564	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708475	0.91[ASN][1000 genomes]
rs11716000	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716007	0.91[ASN][1000 genomes]
rs11716281	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716579	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719660	0.91[ASN][1000 genomes]
rs11914591	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs11916285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs11918243	0.97[ASN][1000 genomes]
rs11918944	0.91[ASN][1000 genomes]
rs11920205	0.91[ASN][1000 genomes]
rs11920327	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11922078	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923486	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923805	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11928233	0.91[ASN][1000 genomes]
rs12203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs13069458	0.91[ASN][1000 genomes]
rs1440154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs1471588	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs17210963	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17212369	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17213336	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17278278	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17852693	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822017	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1827158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs3772100	0.92[EUR][1000 genomes]
rs55650073	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55662129	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730510	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764252	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55988144	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075614	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56290036	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322058	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276861	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276862	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276864	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276869	0.91[ASN][1000 genomes]
rs62276879	0.85[ASN][1000 genomes]
rs62276883	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276884	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276885	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276888	0.91[ASN][1000 genomes]
rs62276909	0.88[ASN][1000 genomes]
rs6440159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6440253	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66517942	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805605	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136038	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73136045	0.91[EUR][1000 genomes]
rs73136048	0.91[EUR][1000 genomes]
rs73136057	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73136060	0.89[EUR][1000 genomes]
rs73138004	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138027	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138030	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138048	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138053	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138055	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138058	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138063	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140009	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73140027	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73140032	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432439	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7614892	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629550	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638009	0.91[ASN][1000 genomes]
rs7642785	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644946	0.93[EUR][1000 genomes]
rs8179927	0.93[EUR][1000 genomes]
rs982291	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	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	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98578000-98601000	Weak transcription	Lung	lung
6	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:98584600-98604200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:98587200-98604600	Weak transcription	Ovary	ovary
10	chr3:98587800-98601800	Strong transcription	HSMM	muscle
11	chr3:98589200-98602200	Weak transcription	NHLF	lung
12	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
13	chr3:98589600-98599800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:98589800-98604000	Weak transcription	Fetal Stomach	stomach
15	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:98590800-98604600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:98591200-98599000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:98591400-98602200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:98591400-98604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:98591600-98600000	Weak transcription	Dnd41	blood
21	chr3:98591600-98604600	Weak transcription	Aorta	Aorta
22	chr3:98592600-98604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:98593200-98599200	Weak transcription	Fetal Brain Female	brain
24	chr3:98593600-98599000	Genic enhancers	NH-A	brain
25	chr3:98593800-98604600	Weak transcription	Psoas Muscle	Psoas
26	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
27	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
28	chr3:98594600-98600600	Strong transcription	HUVEC	blood vessel
29	chr3:98594600-98602200	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:98594600-98604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:98595000-98603600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:98595200-98608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:98595600-98600400	Genic enhancers	NHEK	skin
34	chr3:98595600-98601800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:98595800-98599000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:98596000-98604000	Weak transcription	K562	blood
37	chr3:98596200-98599400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:98596200-98600800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:98596200-98601000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:98596200-98606600	Weak transcription	HepG2	liver
41	chr3:98596600-98600600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:98596800-98604200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:98597000-98600400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:98597000-98600400	Strong transcription	Fetal Lung	lung
45	chr3:98597000-98609000	Weak transcription	Right Ventricle	heart
46	chr3:98597200-98599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:98597200-98600000	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:98597400-98599800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr3:98597600-98602400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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