Variant report

Variant	rs2500409
Chromosome Location	chr20:25400237-25400238
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	chr20:25393485..25396024-chr20:25399784..25401777,2	K562	blood:

Variant related genes	Relation type
ENSG00000101003	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1609701	1.00[ASN][1000 genomes]
rs1888038	1.00[ASN][1000 genomes]
rs2039400	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2210053	1.00[ASN][1000 genomes]
rs2258671	1.00[AMR][1000 genomes]
rs2258672	1.00[AMR][1000 genomes]
rs242122	1.00[ASN][1000 genomes]
rs242124	1.00[ASN][1000 genomes]
rs242125	1.00[ASN][1000 genomes]
rs242131	1.00[ASN][1000 genomes]
rs242134	1.00[ASN][1000 genomes]
rs2474768	1.00[AMR][1000 genomes]
rs2474770	1.00[AMR][1000 genomes]
rs2474772	1.00[AMR][1000 genomes]
rs2474775	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2474776	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2482917	0.83[AFR][1000 genomes];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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	1.00[AMR][1000 genomes]
rs2500412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500434	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	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2892407	1.00[ASN][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002699	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002700	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	1.00[ASN][1000 genomes]
rs378534	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	1.00[ASN][1000 genomes]
rs394798	1.00[ASN][1000 genomes]
rs400916	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	1.00[ASN][1000 genomes]
rs409888	1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs417662	1.00[ASN][1000 genomes]
rs423248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4815433	1.00[ASN][1000 genomes]
rs4815434	1.00[ASN][1000 genomes]
rs518336	1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs57450264	1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037089	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037113	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037119	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037147	1.00[ASN][1000 genomes]
rs6037155	1.00[ASN][1000 genomes]
rs6037160	1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050695	1.00[ASN][1000 genomes]
rs6050711	1.00[ASN][1000 genomes]
rs6076360	1.00[ASN][1000 genomes]
rs6076365	1.00[ASN][1000 genomes]
rs6083882	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[ASN][1000 genomes]
rs7263728	1.00[ASN][1000 genomes]
rs73904036	1.00[AMR][1000 genomes]
rs73904038	1.00[AMR][1000 genomes]
rs73904039	1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs8116049	1.00[ASN][1000 genomes]
rs913790	1.00[ASN][1000 genomes]
rs913791	1.00[ASN][1000 genomes]
rs913793	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	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
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer 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
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25388800-25418000	Weak transcription	Gastric	stomach
2	chr20:25389000-25433600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:25389200-25411000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:25389200-25415000	Weak transcription	Primary B cells from cord blood	blood
5	chr20:25389400-25402400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr20:25389400-25407000	Weak transcription	Fetal Intestine Large	intestine
7	chr20:25389400-25407800	Weak transcription	Fetal Brain Female	brain
8	chr20:25389400-25422800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr20:25389600-25400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:25389600-25426400	Weak transcription	NH-A	brain
11	chr20:25389600-25426600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr20:25389600-25432200	Weak transcription	Fetal Brain Male	brain
13	chr20:25389800-25401200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr20:25389800-25406800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:25389800-25411400	Weak transcription	Fetal Kidney	kidney
16	chr20:25389800-25417000	Weak transcription	Fetal Heart	heart
17	chr20:25389800-25417600	Weak transcription	HSMM	muscle
18	chr20:25389800-25432600	Weak transcription	Esophagus	oesophagus
19	chr20:25390000-25434800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr20:25390200-25406600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:25390200-25416200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr20:25390400-25417400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr20:25390600-25426200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr20:25390600-25433400	Weak transcription	Brain Germinal Matrix	brain
25	chr20:25391000-25418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr20:25391600-25416000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr20:25391600-25416200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr20:25392200-25430800	Strong transcription	Dnd41	blood
29	chr20:25393200-25416400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr20:25393400-25406600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:25393400-25416000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr20:25393400-25416400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr20:25393600-25416400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr20:25394200-25401800	Strong transcription	HepG2	liver
35	chr20:25394200-25416200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr20:25394800-25410400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr20:25395000-25416200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr20:25396000-25401600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr20:25396600-25400400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:25396600-25404200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr20:25397000-25400800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr20:25397600-25402600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:25397800-25402000	Strong transcription	Fetal Stomach	stomach
44	chr20:25398600-25400600	Strong transcription	Fetal Lung	lung
45	chr20:25398800-25400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr20:25398800-25403600	Weak transcription	Fetal Intestine Small	intestine
47	chr20:25398800-25407800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr20:25398800-25429800	Weak transcription	Hela-S3	cervix
49	chr20:25399000-25401800	Strong transcription	Fetal Muscle Leg	muscle
50	chr20:25399600-25406400	Weak transcription	Osteobl	bone

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