Variant report

Variant	rs17012778
Chromosome Location	chr2:33521634-33521635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:33515586..33518253-chr2:33521124..33522863,2	MCF-7	breast:
2	chr2:33521500..33523864-chr2:33524061..33525573,2	K562	blood:
3	chr2:33514241..33517210-chr2:33520355..33523749,3	K562	blood:
4	chr2:33513308..33515964-chr2:33519124..33522873,3	K562	blood:

Variant related genes	Relation type
ENSG00000049323	Chromatin interaction

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

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

rs_ID	r²[population]
rs10048733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10084248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10167324	0.80[ASN][1000 genomes]
rs10167399	0.80[ASN][1000 genomes]
rs10170980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10173416	0.90[ASN][1000 genomes]
rs10189948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10195782	0.80[ASN][1000 genomes]
rs10201015	0.80[ASN][1000 genomes]
rs10201397	0.80[ASN][1000 genomes]
rs10201620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10204479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10205515	0.80[ASN][1000 genomes]
rs10514773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11675702	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11686962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11691887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11692723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11886226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11886337	0.80[ASN][1000 genomes]
rs11898777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13392128	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13408945	0.80[ASN][1000 genomes]
rs13417478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012612	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012621	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012646	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17012657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17012674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17012680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17012691	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17012718	0.80[YRI][hapmap]
rs17012720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17012773	0.81[YRI][hapmap]
rs2004437	0.95[ASN][1000 genomes]
rs2167973	0.82[CEU][hapmap]
rs2290427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2290447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3769546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4578839	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4641915	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs55852365	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57095191	0.80[ASN][1000 genomes]
rs57119251	0.80[ASN][1000 genomes]
rs60523332	0.80[ASN][1000 genomes]
rs61754245	0.90[ASN][1000 genomes]
rs6543696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6543697	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6706122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6722904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6728561	0.80[ASN][1000 genomes]
rs6730341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6734291	0.80[ASN][1000 genomes]
rs6752708	0.80[ASN][1000 genomes]
rs6757287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6757381	0.80[ASN][1000 genomes]
rs6760864	0.90[ASN][1000 genomes]
rs72855746	0.80[ASN][1000 genomes]
rs72855774	0.80[ASN][1000 genomes]
rs72855787	0.80[ASN][1000 genomes]
rs72858037	0.80[ASN][1000 genomes]
rs72858071	0.90[ASN][1000 genomes]
rs72858072	0.90[ASN][1000 genomes]
rs73927364	0.95[ASN][1000 genomes]
rs7583435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7603774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7606937	0.80[ASN][1000 genomes]
rs9308932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs964701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:33505000-33526200	Weak transcription	Placenta	Placenta
5	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:33516400-33522000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:33517000-33522000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:33517000-33522000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:33517000-33522000	Weak transcription	Left Ventricle	heart
10	chr2:33517000-33522800	Weak transcription	K562	blood
11	chr2:33517000-33524600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:33517000-33525400	Weak transcription	Right Ventricle	heart
13	chr2:33517000-33526600	Weak transcription	Fetal Stomach	stomach
14	chr2:33517000-33528800	Weak transcription	Psoas Muscle	Psoas
15	chr2:33517000-33529200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:33517000-33529400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:33517000-33529600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:33517200-33522200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:33517200-33522800	Weak transcription	HSMMtube	muscle
20	chr2:33517200-33525800	Weak transcription	Liver	Liver
21	chr2:33517200-33533000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:33517200-33533200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:33517200-33537400	Weak transcription	Fetal Brain Male	brain
24	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
25	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
26	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:33517600-33532600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:33517600-33532800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:33518200-33522000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:33518200-33522000	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:33518400-33522800	Weak transcription	NHDF-Ad	bronchial
33	chr2:33518600-33521800	Weak transcription	HUVEC	blood vessel
34	chr2:33518600-33522000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:33518600-33522000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:33520400-33522000	Strong transcription	NH-A	brain
37	chr2:33520400-33522200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:33520600-33521800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:33520800-33522000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:33520800-33522000	Genic enhancers	Aorta	Aorta
41	chr2:33520800-33522200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:33520800-33522200	Genic enhancers	Fetal Heart	heart
43	chr2:33520800-33522400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:33520800-33523400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:33521000-33521800	Strong transcription	NHLF	lung
46	chr2:33521000-33523400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:33521000-33523600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:33521400-33521800	Enhancers	Right Atrium	heart
49	chr2:33521400-33521800	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr2:33521400-33522800	Weak transcription	Muscle Satellite Cultured Cells	--

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