Variant report

Variant	rs1888038
Chromosome Location	chr20:25560696-25560697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25560435..25563283-chr20:25564652..25566367,3	MCF-7	breast:
2	chr20:25559789..25563161-chr20:25564263..25567245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1609701	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2210053	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242131	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242134	0.96[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]
rs2482917	1.00[ASN][1000 genomes]
rs2482945	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]
rs2500447	1.00[ASN][1000 genomes]
rs28801689	1.00[ASN][1000 genomes]
rs2892407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2990515	1.00[ASN][1000 genomes]
rs364722	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	1.00[ASN][1000 genomes]
rs368636	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs394798	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs409888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs417662	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs423248	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs429120	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4815434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs518336	0.86[AFR][1000 genomes]
rs55822316	0.84[AFR][1000 genomes];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	0.88[AFR][1000 genomes];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	1.00[ASN][1000 genomes]
rs6037147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037160	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037177	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037185	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037194	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037197	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037200	0.84[AFR][1000 genomes];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	1.00[ASN][1000 genomes]
rs6050618	1.00[ASN][1000 genomes]
rs6050627	1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs6050695	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050735	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050740	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050752	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050759	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050772	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050776	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050786	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050806	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050831	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050837	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050852	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050875	1.00[ASN][1000 genomes]
rs6076360	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6076365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083882	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083883	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6115206	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6132844	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7263728	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904476	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904499	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73907612	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907614	1.00[ASN][1000 genomes]
rs8116049	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913790	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913791	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913793	0.86[AFR][1000 genomes];1.00[AMR][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	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	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
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
2	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
4	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
5	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
7	chr20:25544600-25565000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:25546400-25565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:25548800-25565200	Weak transcription	Esophagus	oesophagus
10	chr20:25550600-25561200	Weak transcription	Gastric	stomach
11	chr20:25552000-25565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr20:25552200-25564800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:25555200-25561200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr20:25555200-25564800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:25555200-25565000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:25555200-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:25555400-25561200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr20:25555400-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr20:25555400-25565000	Weak transcription	Brain Anterior Caudate	brain
20	chr20:25555400-25565000	Weak transcription	NHLF	lung
21	chr20:25557000-25565000	Weak transcription	Thymus	Thymus
22	chr20:25558200-25561400	Weak transcription	Pancreas	Pancrea
23	chr20:25558200-25565200	Weak transcription	Spleen	Spleen
24	chr20:25558800-25561200	Strong transcription	Fetal Brain Female	brain
25	chr20:25559000-25562000	Enhancers	Fetal Heart	heart
26	chr20:25559400-25560800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:25559600-25561000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:25559600-25561200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr20:25559600-25561400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr20:25559600-25561800	Genic enhancers	A549	lung
31	chr20:25560200-25561000	Strong transcription	Dnd41	blood
32	chr20:25560200-25561400	Genic enhancers	Fetal Lung	lung
33	chr20:25560200-25565000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr20:25560400-25560800	Strong transcription	Fetal Intestine Small	intestine
35	chr20:25560400-25561000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr20:25560400-25561000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr20:25560400-25561000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr20:25560400-25561000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:25560400-25561200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr20:25560400-25561400	Strong transcription	Fetal Stomach	stomach
41	chr20:25560400-25561400	Weak transcription	Lung	lung
42	chr20:25560400-25561400	Weak transcription	Ovary	ovary
43	chr20:25560400-25561600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr20:25560400-25564000	Weak transcription	Fetal Brain Male	brain
45	chr20:25560400-25564600	Weak transcription	Brain Germinal Matrix	brain
46	chr20:25560400-25564800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr20:25560400-25564800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr20:25560400-25564800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr20:25560400-25564800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr20:25560400-25564800	Weak transcription	NH-A	brain

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