Variant report

Variant	rs2500396
Chromosome Location	chr20:25349350-25349351
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	chr20:25347572..25351720-chr20:25369390..25373253,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NINL-1	chr20:25348911-25349402	NONHSAT079153

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1609701	1.00[ASN][1000 genomes]
rs2039400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2210053	1.00[ASN][1000 genomes]
rs2258671	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	1.00[AMR][1000 genomes]
rs2474770	1.00[AMR][1000 genomes]
rs2474772	1.00[AMR][1000 genomes]
rs2474775	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2474776	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	0.85[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	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500407	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	1.00[AMR][1000 genomes]
rs2500412	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500419	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500434	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	1.00[ASN][1000 genomes]
rs2500437	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500445	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	0.98[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	1.00[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	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	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	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	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	1.00[AMR][1000 genomes]
rs518336	1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037089	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037119	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs6076360	1.00[ASN][1000 genomes]
rs6115206	1.00[ASN][1000 genomes]
rs6132844	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:17 , 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	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv962567	chr20:25347628-25350309	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
3	chr20:25334600-25353600	Weak transcription	Aorta	Aorta
4	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:25334800-25351000	Weak transcription	Fetal Intestine Small	intestine
6	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr20:25335800-25350200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr20:25337000-25370000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr20:25337400-25355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:25337600-25353600	Weak transcription	Thymus	Thymus
11	chr20:25337600-25354200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:25337600-25362800	Weak transcription	Spleen	Spleen
13	chr20:25337800-25350400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr20:25338000-25369400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:25338200-25350000	Weak transcription	Brain Angular Gyrus	brain
16	chr20:25338200-25359000	Weak transcription	Fetal Intestine Large	intestine
17	chr20:25339400-25349800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr20:25339400-25359600	Weak transcription	Lung	lung
19	chr20:25341800-25357600	Weak transcription	Ovary	ovary
20	chr20:25342200-25353200	Weak transcription	Fetal Lung	lung
21	chr20:25342200-25354600	Weak transcription	Dnd41	blood
22	chr20:25342200-25361800	Weak transcription	Primary B cells from cord blood	blood
23	chr20:25342200-25362600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr20:25342200-25370000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr20:25342400-25355600	Weak transcription	A549	lung
26	chr20:25342400-25357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr20:25343800-25370000	Weak transcription	Small Intestine	intestine
28	chr20:25345200-25369800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr20:25345600-25349600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr20:25345600-25351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:25345600-25353600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr20:25345800-25350000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:25345800-25350200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr20:25345800-25350400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:25345800-25353200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:25345800-25354200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr20:25345800-25357600	Weak transcription	Right Atrium	heart
38	chr20:25345800-25359400	Weak transcription	Left Ventricle	heart
39	chr20:25345800-25359600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr20:25345800-25361600	Weak transcription	K562	blood
41	chr20:25345800-25363200	Weak transcription	Esophagus	oesophagus
42	chr20:25345800-25369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr20:25345800-25370000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr20:25345800-25370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr20:25346200-25357600	Weak transcription	HepG2	liver
46	chr20:25346200-25362800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr20:25346600-25355200	Weak transcription	Gastric	stomach
48	chr20:25347000-25350000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr20:25347200-25349600	Weak transcription	Pancreas	Pancrea
50	chr20:25347600-25357600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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