Variant report

Variant	rs518336
Chromosome Location	chr20:25473471-25473472
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	chr20:25471295..25474295-chr20:25476336..25479406,5	MCF-7	breast:
2	chr20:25445981..25448619-chr20:25473407..25476003,2	K562	blood:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1609701	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs1888038	0.86[AFR][1000 genomes]
rs2039400	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs2210053	1.00[AFR][1000 genomes]
rs242122	0.86[AFR][1000 genomes]
rs242124	0.86[AFR][1000 genomes]
rs242125	0.86[AFR][1000 genomes]
rs242131	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes]
rs242134	0.82[AFR][1000 genomes]
rs2482907	1.00[AMR][1000 genomes]
rs2482909	1.00[AMR][1000 genomes]
rs2482916	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes]
rs2482920	1.00[AMR][1000 genomes]
rs2482922	1.00[AMR][1000 genomes]
rs2482925	1.00[AMR][1000 genomes]
rs2482929	1.00[AMR][1000 genomes]
rs2482939	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs2482942	1.00[AMR][1000 genomes]
rs2482945	1.00[AMR][1000 genomes]
rs2500394	1.00[AMR][1000 genomes]
rs2500396	1.00[AMR][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2500409	1.00[AMR][1000 genomes]
rs2500412	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500414	1.00[AMR][1000 genomes]
rs2500419	1.00[AMR][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500421	1.00[MEX][hapmap]
rs2500429	1.00[AMR][1000 genomes]
rs2500431	1.00[AMR][1000 genomes]
rs2500434	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs2500437	1.00[AMR][1000 genomes]
rs2500438	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs2500440	1.00[AMR][1000 genomes]
rs2500444	1.00[AMR][1000 genomes]
rs2500445	1.00[AMR][1000 genomes]
rs2500447	1.00[AMR][1000 genomes]
rs2892407	0.86[AFR][1000 genomes]
rs2990515	1.00[AMR][1000 genomes]
rs3002699	1.00[AMR][1000 genomes]
rs3002700	1.00[AMR][1000 genomes]
rs3002703	1.00[AMR][1000 genomes]
rs364722	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs366060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs371447	1.00[AFR][1000 genomes]
rs378534	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs379538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs380021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs384336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs388007	0.80[YRI][hapmap];1.00[AFR][1000 genomes]
rs394798	1.00[AFR][1000 genomes]
rs400916	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs409873	1.00[AFR][1000 genomes]
rs409888	1.00[AFR][1000 genomes]
rs417446	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs417662	1.00[AFR][1000 genomes]
rs423248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs428801	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs429120	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs430595	0.89[YRI][hapmap]
rs432403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs439642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs442728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs448212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs448866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4815433	0.86[AFR][1000 genomes]
rs4815434	0.86[AFR][1000 genomes]
rs6037089	1.00[AMR][1000 genomes]
rs6037118	1.00[MEX][hapmap]
rs6037119	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6037147	0.86[AFR][1000 genomes]
rs6037155	0.86[AFR][1000 genomes]
rs6050591	1.00[AMR][1000 genomes]
rs6050613	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050618	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050627	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050628	0.89[AFR][1000 genomes]
rs6050695	0.83[AFR][1000 genomes]
rs6050711	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes]
rs6076360	1.00[AFR][1000 genomes]
rs6076365	0.86[AFR][1000 genomes]
rs6083882	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes]
rs6083883	0.96[AFR][1000 genomes]
rs6083887	0.86[AFR][1000 genomes]
rs6115206	1.00[AFR][1000 genomes]
rs6132844	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes]
rs7263728	0.96[AFR][1000 genomes]
rs73904476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8116049	1.00[AFR][1000 genomes]
rs913790	1.00[AFR][1000 genomes]
rs913791	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes]
rs913793	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
4	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
2	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
3	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr20:25446400-25488200	Weak transcription	Right Atrium	heart
6	chr20:25447000-25477600	Strong transcription	Fetal Muscle Leg	muscle
7	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:25448600-25484200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr20:25448800-25480800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:25451200-25474000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
13	chr20:25457600-25474000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:25457800-25489000	Weak transcription	Placenta	Placenta
15	chr20:25459800-25489800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:25462800-25474800	Weak transcription	Right Ventricle	heart
17	chr20:25462800-25488200	Weak transcription	Colonic Mucosa	Colon
18	chr20:25464000-25474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr20:25464200-25474400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr20:25465000-25483000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr20:25465400-25481600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:25465600-25490000	Weak transcription	Brain Angular Gyrus	brain
23	chr20:25465800-25488000	Weak transcription	Fetal Kidney	kidney
24	chr20:25466000-25484200	Weak transcription	Fetal Brain Male	brain
25	chr20:25466200-25477400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr20:25467400-25484200	Weak transcription	Left Ventricle	heart
27	chr20:25467400-25491800	Weak transcription	Primary T cells from cord blood	blood
28	chr20:25467600-25488000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr20:25467800-25476400	Strong transcription	A549	lung
30	chr20:25468600-25484200	Weak transcription	HUVEC	blood vessel
31	chr20:25469000-25477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr20:25469800-25477400	Weak transcription	HSMMtube	muscle
33	chr20:25469800-25484200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr20:25470000-25475800	Weak transcription	Brain Substantia Nigra	brain
35	chr20:25470000-25477400	Weak transcription	Colon Smooth Muscle	Colon
36	chr20:25470000-25483000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25470000-25488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:25470000-25488000	Weak transcription	Osteobl	bone
39	chr20:25470200-25475600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:25470200-25484200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:25470600-25477400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr20:25470600-25484200	Weak transcription	NHLF	lung
43	chr20:25470800-25480800	Weak transcription	Fetal Lung	lung
44	chr20:25470800-25484200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr20:25470800-25484400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:25471000-25475800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:25471000-25488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr20:25471400-25482400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr20:25471400-25483000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:25471600-25475000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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