Variant report

Variant	rs417446
Chromosome Location	chr20:25514267-25514268
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	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:

Extended variants
information (count: 204 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs1609701	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs1888038	1.00[ASN][1000 genomes]
rs2039400	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2210053	1.00[ASN][1000 genomes]
rs242122	1.00[ASN][1000 genomes]
rs242124	1.00[ASN][1000 genomes]
rs242125	1.00[ASN][1000 genomes]
rs242131	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs242134	1.00[ASN][1000 genomes]
rs2482907	1.00[ASN][1000 genomes]
rs2482909	1.00[ASN][1000 genomes]
rs2482917	1.00[ASN][1000 genomes]
rs2482929	1.00[ASN][1000 genomes]
rs2482939	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2482942	1.00[ASN][1000 genomes]
rs2482945	1.00[ASN][1000 genomes]
rs2500394	1.00[ASN][1000 genomes]
rs2500396	1.00[ASN][1000 genomes]
rs2500407	1.00[ASN][1000 genomes]
rs2500409	1.00[ASN][1000 genomes]
rs2500412	1.00[ASN][1000 genomes]
rs2500414	1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[ASN][1000 genomes]
rs2500421	1.00[MEX][hapmap]
rs2500444	1.00[ASN][1000 genomes]
rs2500445	1.00[ASN][1000 genomes]
rs2500447	1.00[ASN][1000 genomes]
rs28417591	1.00[EUR][1000 genomes]
rs28439563	1.00[EUR][1000 genomes]
rs28733778	1.00[EUR][1000 genomes]
rs28801689	1.00[ASN][1000 genomes]
rs2892407	1.00[ASN][1000 genomes]
rs2990515	1.00[ASN][1000 genomes]
rs3002703	1.00[ASN][1000 genomes]
rs364722	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs366060	1.00[ASN][1000 genomes]
rs368636	1.00[ASN][1000 genomes]
rs368748	1.00[ASN][1000 genomes]
rs371447	1.00[ASN][1000 genomes]
rs378534	1.00[ASN][1000 genomes]
rs379538	1.00[ASN][1000 genomes]
rs380021	1.00[ASN][1000 genomes]
rs384336	1.00[ASN][1000 genomes]
rs388007	1.00[ASN][1000 genomes]
rs394798	1.00[ASN][1000 genomes]
rs400916	1.00[ASN][1000 genomes]
rs409873	1.00[ASN][1000 genomes]
rs409888	1.00[ASN][1000 genomes]
rs417662	1.00[ASN][1000 genomes]
rs423248	1.00[ASN][1000 genomes]
rs426143	1.00[ASN][1000 genomes]
rs428801	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs429120	1.00[ASN][1000 genomes]
rs432403	1.00[ASN][1000 genomes]
rs439642	1.00[ASN][1000 genomes]
rs442728	1.00[ASN][1000 genomes]
rs448212	1.00[ASN][1000 genomes]
rs4815433	1.00[ASN][1000 genomes]
rs4815434	1.00[ASN][1000 genomes]
rs518336	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs55822316	1.00[ASN][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs56751491	1.00[ASN][1000 genomes]
rs56795563	1.00[EUR][1000 genomes]
rs57237389	1.00[EUR][1000 genomes]
rs57450264	1.00[ASN][1000 genomes]
rs57522322	1.00[EUR][1000 genomes]
rs57579912	1.00[EUR][1000 genomes]
rs58189090	1.00[EUR][1000 genomes]
rs58410604	1.00[EUR][1000 genomes]
rs58722006	1.00[EUR][1000 genomes]
rs59122217	1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs59362331	1.00[EUR][1000 genomes]
rs59826126	1.00[EUR][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037118	1.00[MEX][hapmap]
rs6037119	1.00[ASN][1000 genomes]
rs6037147	1.00[ASN][1000 genomes]
rs6037155	1.00[ASN][1000 genomes]
rs6037160	1.00[ASN][1000 genomes]
rs6037172	1.00[ASN][1000 genomes]
rs6037177	1.00[ASN][1000 genomes]
rs6037185	1.00[ASN][1000 genomes]
rs6037194	1.00[ASN][1000 genomes]
rs6037197	1.00[ASN][1000 genomes]
rs6037200	1.00[ASN][1000 genomes]
rs6037209	1.00[ASN][1000 genomes]
rs6037213	1.00[ASN][1000 genomes]
rs60459445	1.00[EUR][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[ASN][1000 genomes]
rs6050613	1.00[ASN][1000 genomes]
rs6050618	1.00[ASN][1000 genomes]
rs6050627	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs6050695	1.00[ASN][1000 genomes]
rs6050711	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6050735	1.00[ASN][1000 genomes]
rs6050740	1.00[ASN][1000 genomes]
rs6050752	1.00[ASN][1000 genomes]
rs6050759	1.00[ASN][1000 genomes]
rs6050772	1.00[ASN][1000 genomes]
rs6050776	1.00[ASN][1000 genomes]
rs6050786	1.00[ASN][1000 genomes]
rs6050806	1.00[ASN][1000 genomes]
rs6050831	1.00[ASN][1000 genomes]
rs6050837	1.00[ASN][1000 genomes]
rs6050839	1.00[ASN][1000 genomes]
rs6050852	1.00[ASN][1000 genomes]
rs6050875	1.00[ASN][1000 genomes]
rs60758360	1.00[EUR][1000 genomes]
rs6076360	1.00[ASN][1000 genomes]
rs6076365	1.00[ASN][1000 genomes]
rs60772859	1.00[EUR][1000 genomes]
rs60831246	1.00[EUR][1000 genomes]
rs60834749	1.00[EUR][1000 genomes]
rs6083882	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6083883	1.00[ASN][1000 genomes]
rs6083887	1.00[ASN][1000 genomes]
rs6115206	1.00[ASN][1000 genomes]
rs6132844	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7263728	1.00[ASN][1000 genomes]
rs7264066	1.00[EUR][1000 genomes]
rs7267807	1.00[EUR][1000 genomes]
rs7274976	1.00[EUR][1000 genomes]
rs73331819	1.00[EUR][1000 genomes]
rs73331822	1.00[EUR][1000 genomes]
rs73331824	1.00[EUR][1000 genomes]
rs73331833	1.00[EUR][1000 genomes]
rs73331834	1.00[EUR][1000 genomes]
rs73331856	1.00[EUR][1000 genomes]
rs73331880	1.00[EUR][1000 genomes]
rs73331881	1.00[EUR][1000 genomes]
rs73333506	1.00[EUR][1000 genomes]
rs73333515	1.00[EUR][1000 genomes]
rs73333541	1.00[EUR][1000 genomes]
rs73333553	1.00[EUR][1000 genomes]
rs73333566	1.00[EUR][1000 genomes]
rs73333583	1.00[EUR][1000 genomes]
rs73333590	1.00[EUR][1000 genomes]
rs73335304	1.00[EUR][1000 genomes]
rs73335318	1.00[EUR][1000 genomes]
rs73335329	1.00[EUR][1000 genomes]
rs73335331	1.00[EUR][1000 genomes]
rs73335348	1.00[EUR][1000 genomes]
rs73335353	1.00[EUR][1000 genomes]
rs73335363	1.00[EUR][1000 genomes]
rs73335366	1.00[EUR][1000 genomes]
rs73335375	1.00[EUR][1000 genomes]
rs73335382	1.00[EUR][1000 genomes]
rs73335383	1.00[EUR][1000 genomes]
rs73335389	1.00[EUR][1000 genomes]
rs73335394	1.00[EUR][1000 genomes]
rs73335398	1.00[EUR][1000 genomes]
rs73335400	1.00[EUR][1000 genomes]
rs73335402	1.00[EUR][1000 genomes]
rs73337303	1.00[EUR][1000 genomes]
rs73337317	1.00[EUR][1000 genomes]
rs73337328	1.00[EUR][1000 genomes]
rs73337360	1.00[EUR][1000 genomes]
rs73337362	1.00[EUR][1000 genomes]
rs73337380	1.00[EUR][1000 genomes]
rs73337391	1.00[EUR][1000 genomes]
rs73339340	1.00[EUR][1000 genomes]
rs73339342	1.00[EUR][1000 genomes]
rs73339354	1.00[EUR][1000 genomes]
rs73339363	1.00[EUR][1000 genomes]
rs73339381	1.00[EUR][1000 genomes]
rs73345087	1.00[EUR][1000 genomes]
rs73345088	1.00[EUR][1000 genomes]
rs73347023	1.00[EUR][1000 genomes]
rs73347042	1.00[EUR][1000 genomes]
rs73347058	1.00[EUR][1000 genomes]
rs73904476	1.00[ASN][1000 genomes]
rs73904499	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs73907612	1.00[ASN][1000 genomes]
rs73907614	1.00[ASN][1000 genomes]
rs8116049	1.00[ASN][1000 genomes]
rs8118017	1.00[EUR][1000 genomes]
rs913790	1.00[ASN][1000 genomes]
rs913791	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs913793	1.00[ASN][1000 genomes]
rs9941767	1.00[EUR][1000 genomes]
rs9967947	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
4	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr20:25498200-25519400	Weak transcription	Gastric	stomach
6	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
9	chr20:25505400-25514600	Weak transcription	Lung	lung
10	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:25507400-25518400	Weak transcription	A549	lung
12	chr20:25507600-25518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
14	chr20:25507800-25516800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr20:25511200-25517600	Weak transcription	Fetal Brain Female	brain
16	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
17	chr20:25512000-25516000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:25512200-25515400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr20:25512200-25515800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr20:25512400-25514400	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr20:25512400-25515000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr20:25512400-25515600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:25512400-25516000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr20:25512400-25516000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:25512600-25515000	Enhancers	Fetal Muscle Leg	muscle
26	chr20:25512600-25515200	Enhancers	Right Ventricle	heart
27	chr20:25512600-25515800	Enhancers	Fetal Heart	heart
28	chr20:25512800-25514400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:25512800-25514400	Enhancers	Adipose Nuclei	Adipose
30	chr20:25512800-25514400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr20:25512800-25514400	Flanking Active TSS	Osteobl	bone
32	chr20:25512800-25514800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr20:25512800-25514800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr20:25512800-25514800	Enhancers	Right Atrium	heart
35	chr20:25512800-25515400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr20:25512800-25515600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr20:25512800-25516000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr20:25513000-25514400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr20:25513000-25515200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr20:25513000-25515800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr20:25513000-25516000	Enhancers	Fetal Thymus	thymus
42	chr20:25513200-25515400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr20:25513200-25516000	Enhancers	HepG2	liver
44	chr20:25513200-25517400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr20:25513400-25514400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr20:25513400-25517000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr20:25513400-25517000	Enhancers	Fetal Lung	lung
48	chr20:25513400-25519200	Enhancers	Liver	Liver
49	chr20:25513600-25514400	Enhancers	NHLF	lung
50	chr20:25513600-25514600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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