Variant report

Variant	rs73614590
Chromosome Location	chr20:25337214-25337215
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	chr20:25328148..25330867-chr20:25336121..25338656,2	MCF-7	breast:
2	chr20:25334830..25338247-chr20:25338696..25341660,3	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10485776	0.84[EUR][1000 genomes]
rs1109100	0.84[EUR][1000 genomes]
rs16987767	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16987786	0.84[EUR][1000 genomes]
rs16987789	0.82[EUR][1000 genomes]
rs16987799	0.84[EUR][1000 genomes]
rs16987820	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2179458	0.84[EUR][1000 genomes]
rs2227894	0.81[ASN][1000 genomes]
rs2424719	0.82[EUR][1000 genomes]
rs35666277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs400070	0.84[EUR][1000 genomes]
rs402120	0.82[EUR][1000 genomes]
rs409401	0.82[EUR][1000 genomes]
rs426563	0.82[EUR][1000 genomes]
rs428278	0.82[EUR][1000 genomes]
rs440612	0.84[EUR][1000 genomes]
rs447808	0.82[EUR][1000 genomes]
rs45587239	0.81[ASN][1000 genomes]
rs4813570	0.84[EUR][1000 genomes]
rs58184048	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58351126	1.00[ASN][1000 genomes]
rs59324912	0.84[EUR][1000 genomes]
rs59546510	0.84[EUR][1000 genomes]
rs6037128	0.84[EUR][1000 genomes]
rs6037131	0.84[EUR][1000 genomes]
rs6037133	0.84[EUR][1000 genomes]
rs6050513	0.81[ASN][1000 genomes]
rs6050515	0.81[ASN][1000 genomes]
rs6050594	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6050597	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6050628	0.82[EUR][1000 genomes]
rs6050651	0.84[EUR][1000 genomes]
rs6050658	0.84[EUR][1000 genomes]
rs6050663	0.84[EUR][1000 genomes]
rs66467007	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66501707	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66591653	0.84[EUR][1000 genomes]
rs66673357	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66927803	0.95[EUR][1000 genomes]
rs66940055	0.95[EUR][1000 genomes]
rs67069812	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67184896	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67359112	0.84[EUR][1000 genomes]
rs67455519	0.84[EUR][1000 genomes]
rs67482703	0.84[EUR][1000 genomes]
rs67679582	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67680401	0.95[EUR][1000 genomes]
rs67867367	0.81[ASN][1000 genomes]
rs67921634	0.84[EUR][1000 genomes]
rs7260843	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7262450	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7266130	0.84[EUR][1000 genomes]
rs7272959	0.94[ASN][1000 genomes]
rs7273525	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73331863	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73331878	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73333512	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73333513	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73597810	0.84[EUR][1000 genomes]
rs73597812	0.84[EUR][1000 genomes]
rs73597813	0.84[EUR][1000 genomes]
rs73598373	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73612664	0.81[ASN][1000 genomes]
rs73612665	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73614591	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73614592	0.81[ASN][1000 genomes]
rs73614594	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs742435	0.84[EUR][1000 genomes]
rs742436	0.84[EUR][1000 genomes]
rs8115484	0.95[EUR][1000 genomes]
rs8115742	0.84[EUR][1000 genomes]
rs8117181	0.84[EUR][1000 genomes]
rs8117253	0.95[EUR][1000 genomes]
rs8124539	0.81[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs73614590	RP4-694B14.5	cis	Thyroid	GTEx
rs73614590	ZNF337	cis	lung	GTEx
rs73614590	ZNF337	cis	Thyroid	GTEx
rs73614590	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs73614590	RP4-694B14.5	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
4	chr20:25332200-25337400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr20:25333400-25338800	Enhancers	Brain Substantia Nigra	brain
6	chr20:25333600-25339200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr20:25333600-25339400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr20:25334000-25338000	Enhancers	Brain Anterior Caudate	brain
9	chr20:25334000-25338600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr20:25334000-25339000	Enhancers	Pancreas	Pancrea
11	chr20:25334000-25339400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:25334200-25337400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr20:25334200-25337400	Enhancers	A549	lung
14	chr20:25334200-25338000	Enhancers	Left Ventricle	heart
15	chr20:25334200-25338000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr20:25334200-25339200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr20:25334200-25339400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr20:25334200-25339600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr20:25334600-25339200	Weak transcription	Esophagus	oesophagus
20	chr20:25334600-25339200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr20:25334600-25341600	Weak transcription	NHLF	lung
22	chr20:25334600-25353600	Weak transcription	Aorta	Aorta
23	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
24	chr20:25334800-25351000	Weak transcription	Fetal Intestine Small	intestine
25	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr20:25335000-25337400	Weak transcription	Gastric	stomach
27	chr20:25335000-25339000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr20:25335200-25339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr20:25335600-25338000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr20:25335600-25341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr20:25335800-25337400	Enhancers	Fetal Brain Male	brain
32	chr20:25335800-25337800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr20:25335800-25341400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr20:25335800-25350200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr20:25336000-25337600	Enhancers	Primary hematopoietic stem cells	blood
36	chr20:25336000-25338800	Enhancers	GM12878-XiMat	blood
37	chr20:25336000-25339400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:25336000-25341400	Weak transcription	Fetal Lung	lung
39	chr20:25336200-25341400	Weak transcription	Primary B cells from cord blood	blood
40	chr20:25336400-25337800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:25336400-25338000	Enhancers	Fetal Brain Female	brain
42	chr20:25336600-25337400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:25336600-25337400	Strong transcription	Fetal Stomach	stomach
44	chr20:25336600-25337600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr20:25336600-25337600	Enhancers	Right Atrium	heart
46	chr20:25336600-25337600	Enhancers	Spleen	Spleen
47	chr20:25336600-25337800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr20:25336600-25338000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr20:25336600-25338200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr20:25336600-25338200	Enhancers	Right Ventricle	heart

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