Variant report

Variant	rs439642
Chromosome Location	chr20:25496997-25496998
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25491958..25494931-chr20:25496004..25498993,2	MCF-7	breast:
2	chr20:25476872..25479818-chr20:25496364..25499002,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1609701	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1888038	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2039400	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2210053	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs242122	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs242124	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs242125	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs242131	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs242134	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482920	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482922	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500412	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500434	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	1.00[ASN][1000 genomes]
rs2500437	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500445	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28801689	1.00[ASN][1000 genomes]
rs2892407	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2990515	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs394798	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs409888	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs417662	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs423248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs429120	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs430595	0.85[YRI][hapmap]
rs432403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4815433	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815434	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs518336	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55822316	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[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037089	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037147	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037155	0.86[AFR][1000 genomes];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]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][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[ASN][1000 genomes]
rs6050711	0.82[AFR][1000 genomes];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]
rs6076360	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6076365	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083882	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083883	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083887	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6115206	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6132844	0.98[AFR][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[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73904499	1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	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[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913790	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913791	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913793	1.00[AFR][1000 genomes];1.00[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25475400-25498000	Weak transcription	Right Ventricle	heart
2	chr20:25485800-25498600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:25487200-25498200	Strong transcription	Stomach Smooth Muscle	stomach
4	chr20:25489400-25505800	Weak transcription	NHDF-Ad	bronchial
5	chr20:25491200-25506200	Weak transcription	NHLF	lung
6	chr20:25492200-25497200	Weak transcription	Fetal Kidney	kidney
7	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
8	chr20:25493400-25499000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:25493600-25498200	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
11	chr20:25494000-25499000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25494000-25502000	ZNF genes & repeats	Dnd41	blood
13	chr20:25494200-25498200	ZNF genes & repeats	Thymus	Thymus
14	chr20:25494400-25497600	ZNF genes & repeats	Fetal Intestine Large	intestine
15	chr20:25494400-25499000	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr20:25494400-25499000	ZNF genes & repeats	Fetal Brain Female	brain
17	chr20:25494400-25499200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr20:25494600-25497400	ZNF genes & repeats	Fetal Lung	lung
19	chr20:25494600-25497600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr20:25494600-25497600	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr20:25494600-25498000	ZNF genes & repeats	HepG2	liver
22	chr20:25494600-25498200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr20:25494600-25498200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
24	chr20:25494600-25498200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr20:25494600-25498200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr20:25494800-25497400	ZNF genes & repeats	Fetal Brain Male	brain
27	chr20:25494800-25497400	ZNF genes & repeats	Ovary	ovary
28	chr20:25494800-25497600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
29	chr20:25494800-25497600	ZNF genes & repeats	A549	lung
30	chr20:25494800-25497800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr20:25494800-25498000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr20:25494800-25498200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
33	chr20:25494800-25498200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:25494800-25498200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr20:25494800-25498200	ZNF genes & repeats	Fetal Stomach	stomach
36	chr20:25495000-25497800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr20:25495000-25498200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:25495200-25498000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr20:25495200-25498200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:25495200-25498200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
41	chr20:25495200-25498200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr20:25495200-25498200	ZNF genes & repeats	Fetal Thymus	thymus
43	chr20:25495600-25497000	Weak transcription	Primary T cells from cord blood	blood
44	chr20:25495600-25504800	Weak transcription	Osteobl	bone
45	chr20:25495800-25497200	Weak transcription	Colonic Mucosa	Colon
46	chr20:25495800-25497200	Weak transcription	Esophagus	oesophagus
47	chr20:25495800-25497200	Weak transcription	HSMMtube	muscle
48	chr20:25495800-25497400	Strong transcription	Rectal Smooth Muscle	rectum
49	chr20:25495800-25497800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr20:25495800-25498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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