Variant report

Variant	rs417662
Chromosome Location	chr20:25513020-25513021
allele	A/G
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:
2	chr20:25499922..25502486-chr20:25510143..25513350,3	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1609701	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1888038	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2039400	1.00[ASN][1000 genomes]
rs2210053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242122	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242124	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242125	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242131	0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242134	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[ASN][1000 genomes]
rs2482909	1.00[ASN][1000 genomes]
rs2482916	0.81[AFR][1000 genomes]
rs2482917	1.00[ASN][1000 genomes]
rs2482925	1.00[ASN][1000 genomes]
rs2482929	1.00[ASN][1000 genomes]
rs2482939	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	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2500409	1.00[ASN][1000 genomes]
rs2500412	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[ASN][1000 genomes]
rs2500440	1.00[ASN][1000 genomes]
rs2500444	1.00[ASN][1000 genomes]
rs2500445	1.00[ASN][1000 genomes]
rs2500447	1.00[ASN][1000 genomes]
rs28801689	1.00[ASN][1000 genomes]
rs2892407	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2990515	1.00[ASN][1000 genomes]
rs3002703	1.00[ASN][1000 genomes]
rs364722	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs394798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs409888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs423248	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs429120	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs430595	0.82[YRI][hapmap]
rs432403	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	0.88[AFR][1000 genomes]
rs4815433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4815434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs518336	1.00[AFR][1000 genomes]
rs55822316	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs56751491	1.00[ASN][1000 genomes]
rs57450264	1.00[ASN][1000 genomes]
rs59122217	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037147	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037155	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037160	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037172	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037177	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037185	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037194	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037197	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037200	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037209	1.00[ASN][1000 genomes]
rs6037213	1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[ASN][1000 genomes]
rs6050613	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050695	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050711	0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050735	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050740	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050752	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050772	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050776	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050786	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050806	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050831	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050837	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050839	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050852	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050875	1.00[ASN][1000 genomes]
rs6076360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6076365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083882	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083887	0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6115206	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6132844	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7263728	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904476	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904499	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs73907612	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907614	1.00[ASN][1000 genomes]
rs8116049	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913791	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
17	nsv979406	chr20:25509600-25513942	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 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	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
3	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
5	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr20:25498200-25519400	Weak transcription	Gastric	stomach
7	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
10	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
12	chr20:25505400-25514600	Weak transcription	Lung	lung
13	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
15	chr20:25507400-25518400	Weak transcription	A549	lung
16	chr20:25507600-25513400	Weak transcription	Liver	Liver
17	chr20:25507600-25513600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr20:25507600-25513600	Weak transcription	NHLF	lung
19	chr20:25507600-25518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
21	chr20:25507800-25513200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:25507800-25516800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:25509000-25513200	Weak transcription	HepG2	liver
24	chr20:25511200-25517600	Weak transcription	Fetal Brain Female	brain
25	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
26	chr20:25511600-25513400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:25512000-25516000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:25512200-25513200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:25512200-25513200	ZNF genes & repeats	Fetal Stomach	stomach
30	chr20:25512200-25514000	ZNF genes & repeats	Dnd41	blood
31	chr20:25512200-25515400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25512200-25515800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr20:25512400-25513200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr20:25512400-25513200	Enhancers	Brain Substantia Nigra	brain
35	chr20:25512400-25514200	Enhancers	Brain Angular Gyrus	brain
36	chr20:25512400-25514200	Enhancers	Fetal Muscle Trunk	muscle
37	chr20:25512400-25514400	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr20:25512400-25515000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr20:25512400-25515600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:25512400-25516000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr20:25512400-25516000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr20:25512600-25513200	Weak transcription	Spleen	Spleen
43	chr20:25512600-25513400	Weak transcription	Thymus	Thymus
44	chr20:25512600-25513600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr20:25512600-25513800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:25512600-25513800	Enhancers	Ovary	ovary
47	chr20:25512600-25515000	Enhancers	Fetal Muscle Leg	muscle
48	chr20:25512600-25515200	Enhancers	Right Ventricle	heart
49	chr20:25512600-25515800	Enhancers	Fetal Heart	heart
50	chr20:25512800-25513400	Active TSS	Aorta	Aorta

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