Variant report

Variant	rs3825616
Chromosome Location	chr14:55853288-55853289
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55851517..55854050-chr14:55862955..55864558,2	K562	blood:
2	chr14:55697987..55700374-chr14:55851952..55854394,2	K562	blood:
3	chr14:55851134..55854346-chr14:55857455..55859971,3	K562	blood:
4	chr14:55832794..55835676-chr14:55852395..55854057,2	K562	blood:
5	chr14:55831903..55834657-chr14:55852806..55855439,2	MCF-7	breast:
6	chr14:55851395..55854155-chr14:55863478..55865665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126775	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10129505	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10131562	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10131730	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10131913	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10131926	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10132453	0.82[ASN][1000 genomes]
rs10134317	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10134339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10136596	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10137307	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139000	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139083	0.81[EUR][1000 genomes]
rs10140801	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs10140869	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs10141396	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10141483	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10141552	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10142448	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10142547	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10142823	0.81[AMR][1000 genomes]
rs10144345	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10144418	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145203	0.83[EUR][1000 genomes]
rs10146637	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10147765	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10149420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10150699	0.80[AMR][1000 genomes]
rs10150760	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1045002	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1045004	0.81[JPT][hapmap]
rs10467798	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1109170	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11158034	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11158037	0.83[ASN][1000 genomes]
rs11621265	0.81[JPT][hapmap]
rs11625001	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11625423	0.84[EUR][1000 genomes]
rs11625968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11626751	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11628437	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs11851169	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12050123	0.82[ASN][1000 genomes]
rs13379169	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1572611	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17128440	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17674463	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17674563	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17740741	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs17741542	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs17741831	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1815580	0.91[EUR][1000 genomes]
rs1815581	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1952087	0.83[AFR][1000 genomes]
rs1972221	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2009291	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2016931	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2026633	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2182797	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2209808	0.91[EUR][1000 genomes]
rs2297816	0.83[ASN][1000 genomes]
rs2341621	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2341622	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28428911	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28430823	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28452705	0.84[ASN][1000 genomes]
rs28493647	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28568813	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28612464	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28631821	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28660594	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28716725	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2880103	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3742569	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3783648	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783649	0.82[ASN][1000 genomes]
rs3783650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3783651	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3783652	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4366639	0.84[EUR][1000 genomes]
rs4496026	0.84[EUR][1000 genomes]
rs4597235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56270323	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56949365	0.83[EUR][1000 genomes]
rs58296156	0.82[ASN][1000 genomes]
rs59629906	0.80[EUR][1000 genomes]
rs59871474	0.80[EUR][1000 genomes]
rs61210954	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6573009	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6573010	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6573013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6573014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6573017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6573020	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66486619	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67412516	0.84[ASN][1000 genomes]
rs7142857	0.82[AMR][1000 genomes]
rs7144292	0.82[AMR][1000 genomes]
rs7144737	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7145727	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146748	0.82[EUR][1000 genomes]
rs7146752	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7147136	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7147247	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7148171	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7150763	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7151581	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7152390	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7153110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153612	0.83[EUR][1000 genomes]
rs7154831	0.82[ASN][1000 genomes]
rs7154889	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7155954	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7158768	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7158791	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7159144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7159824	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7161439	0.84[ASN][1000 genomes]
rs72717738	0.84[ASN][1000 genomes]
rs8005450	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs8006525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8008119	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8013713	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8014477	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8014540	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs8015211	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8021583	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs8022041	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8022225	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8023197	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9323284	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323285	0.81[JPT][hapmap]
rs943590	0.81[EUR][1000 genomes]
rs946059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9919923	0.82[ASN][1000 genomes]
rs9919926	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9919932	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv901957	chr14:55819219-55853724	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3825616	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55808800-55865200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:55818200-55877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:55818400-55858800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:55819400-55855200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:55821400-55865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:55831000-55859400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr14:55831800-55858000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr14:55832400-55857800	Strong transcription	Liver	Liver
9	chr14:55836800-55877800	Weak transcription	Esophagus	oesophagus
10	chr14:55838600-55853600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:55839400-55859200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr14:55839600-55858600	Strong transcription	Primary B cells from peripheral blood	blood
13	chr14:55840200-55858800	Strong transcription	Primary B cells from cord blood	blood
14	chr14:55840400-55856600	Strong transcription	Fetal Intestine Large	intestine
15	chr14:55840400-55856800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:55840600-55854200	Strong transcription	Brain Cingulate Gyrus	brain
17	chr14:55841000-55859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:55841800-55855000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr14:55842000-55856200	Strong transcription	Fetal Muscle Leg	muscle
20	chr14:55842200-55856400	Strong transcription	Placenta	Placenta
21	chr14:55842400-55854200	Strong transcription	Brain Hippocampus Middle	brain
22	chr14:55842400-55855400	Strong transcription	Fetal Stomach	stomach
23	chr14:55842600-55853400	Strong transcription	Lung	lung
24	chr14:55843400-55853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:55843600-55855000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:55844000-55854800	Weak transcription	Fetal Brain Male	brain
27	chr14:55845000-55855200	Strong transcription	Fetal Intestine Small	intestine
28	chr14:55846000-55854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:55847200-55855400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr14:55847200-55856800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:55848600-55856200	Strong transcription	HepG2	liver
32	chr14:55848600-55876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr14:55848800-55854800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr14:55848800-55855000	Weak transcription	HMEC	breast
35	chr14:55848800-55855800	Weak transcription	Brain Angular Gyrus	brain
36	chr14:55848800-55861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:55848800-55861200	Weak transcription	Small Intestine	intestine
38	chr14:55848800-55861800	Weak transcription	HUVEC	blood vessel
39	chr14:55848800-55864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr14:55848800-55865000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr14:55849000-55855000	Weak transcription	NHDF-Ad	bronchial
42	chr14:55849000-55856000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr14:55849200-55876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr14:55849200-55878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:55849600-55855800	Weak transcription	Fetal Lung	lung
46	chr14:55849800-55865200	Weak transcription	A549	lung
47	chr14:55850000-55853400	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr14:55850000-55853400	Weak transcription	NHLF	lung
49	chr14:55850000-55868400	Weak transcription	Right Ventricle	heart
50	chr14:55850200-55853800	Weak transcription	Brain Anterior Caudate	brain

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