Variant report

Variant	rs2500430
Chromosome Location	chr20:25278963-25278964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25277010..25279912-chr20:25462998..25464763,2	K562	blood:
2	chr20:25277532..25280083-chr20:25374458..25376489,2	K562	blood:
3	chr20:25277853..25279488-chr20:25281657..25283835,2	MCF-7	breast:
4	chr20:25275341..25277928-chr20:25277933..25279564,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1046073	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1077889	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10966	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11100	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1555329	0.80[EUR][1000 genomes]
rs1888998	0.81[EUR][1000 genomes]
rs1888999	0.81[EUR][1000 genomes]
rs2145126	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2227890	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2227892	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257233	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257420	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257432	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257461	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257464	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2257496	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257649	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2257705	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257712	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257808	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257809	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257982	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257985	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2257988	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257991	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258066	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258135	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2258201	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258563	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258617	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258719	0.81[EUR][1000 genomes]
rs2258728	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2258769	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258879	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2258884	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2259837	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2259873	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2259926	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2259928	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2259956	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2259961	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2261109	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261115	0.80[AMR][1000 genomes]
rs2261698	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261720	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2261753	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261784	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261785	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261790	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2261794	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2261796	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2297496	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2297497	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2424700	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2424703	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2424704	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2424708	0.81[EUR][1000 genomes]
rs2424710	0.81[EUR][1000 genomes]
rs2424711	0.81[EUR][1000 genomes]
rs2474763	0.81[EUR][1000 genomes]
rs2474765	0.90[EUR][1000 genomes]
rs2474777	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2474780	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2500413	0.81[EUR][1000 genomes]
rs2500432	0.81[EUR][1000 genomes]
rs2983489	0.90[EUR][1000 genomes]
rs3002702	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs33999482	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35735333	0.88[EUR][1000 genomes]
rs3787082	0.80[EUR][1000 genomes]
rs4355182	0.80[EUR][1000 genomes]
rs4813557	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4815400	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4815405	0.90[AFR][1000 genomes]
rs4815413	0.86[EUR][1000 genomes]
rs6037083	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6037085	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6050498	0.80[EUR][1000 genomes]
rs6050532	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6050542	0.90[AFR][1000 genomes]
rs6050547	0.90[AFR][1000 genomes]
rs6050561	0.84[AFR][1000 genomes]
rs6076336	0.90[AFR][1000 genomes]
rs6076343	0.80[EUR][1000 genomes]
rs6083799	0.89[AFR][1000 genomes]
rs6083801	0.90[AFR][1000 genomes]
rs6083804	0.90[AFR][1000 genomes]
rs6083809	0.84[AFR][1000 genomes]
rs6083813	0.84[AFR][1000 genomes]
rs6083824	0.86[EUR][1000 genomes]
rs6083845	0.80[EUR][1000 genomes]
rs6107027	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6115107	0.81[EUR][1000 genomes]
rs6115140	0.81[EUR][1000 genomes]
rs6115146	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6115153	0.84[AFR][1000 genomes]
rs6115156	0.87[EUR][1000 genomes]
rs6132825	0.83[EUR][1000 genomes]
rs66999585	0.80[AMR][1000 genomes]
rs7019	0.81[EUR][1000 genomes]
rs7267979	0.80[AMR][1000 genomes]
rs7343481	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs869358	0.80[EUR][1000 genomes]
rs884613	0.81[EUR][1000 genomes]
rs910996	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs910997	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9927	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
18	nsv912827	chr20:25271326-25288632	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2500430	NINL	cis	Thyroid	GTEx
rs2500430	PYGB	cis	Whole Blood	GTEx
rs2500430	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2500430	ABHD12	cis	Nerve Tibial	GTEx
rs2500430	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs2500430	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr20:25249200-25285800	Strong transcription	Dnd41	blood
5	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
10	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr20:25254400-25287800	Weak transcription	K562	blood
12	chr20:25255600-25279200	Strong transcription	Fetal Brain Female	brain
13	chr20:25255800-25290000	Weak transcription	Small Intestine	intestine
14	chr20:25256000-25299400	Weak transcription	Fetal Brain Male	brain
15	chr20:25259000-25290800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:25261600-25291000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:25266600-25291200	Weak transcription	Primary B cells from cord blood	blood
18	chr20:25267000-25291200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr20:25267600-25279200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr20:25269200-25281600	Weak transcription	Liver	Liver
21	chr20:25271400-25279600	Genic enhancers	HMEC	breast
22	chr20:25271400-25290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr20:25271600-25291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:25272800-25282400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr20:25273400-25287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:25274800-25280800	Weak transcription	Aorta	Aorta
27	chr20:25275000-25283400	Genic enhancers	A549	lung
28	chr20:25275400-25285600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:25275600-25279200	Genic enhancers	Brain Hippocampus Middle	brain
30	chr20:25275600-25280600	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr20:25275600-25290400	Strong transcription	Fetal Stomach	stomach
32	chr20:25275800-25285200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr20:25275800-25290600	Strong transcription	Thymus	Thymus
34	chr20:25276000-25279600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:25276200-25280200	Strong transcription	Osteobl	bone
36	chr20:25276200-25281800	Strong transcription	Fetal Lung	lung
37	chr20:25276200-25285000	Strong transcription	Spleen	Spleen
38	chr20:25276200-25285200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr20:25276200-25285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr20:25276200-25285200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:25276600-25279800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr20:25276600-25282400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr20:25276800-25279600	Strong transcription	NH-A	brain
44	chr20:25276800-25280600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr20:25276800-25284600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr20:25276800-25285000	Strong transcription	Primary T cells from cord blood	blood
47	chr20:25277000-25280200	Weak transcription	HSMM	muscle
48	chr20:25277000-25285600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr20:25277200-25282200	Weak transcription	Right Atrium	heart
50	chr20:25277200-25284000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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