Variant report

Variant	rs11625968
Chromosome Location	chr14:55801004-55801005
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55799382..55802320-chr14:55805290..55807790,2	K562	blood:
2	chr14:55795389..55798237-chr14:55800150..55802367,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258455	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1009978	0.84[CEU][hapmap]
rs10129505	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10131562	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10131730	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10131913	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10134317	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10134339	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10136596	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs10137307	0.91[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs10139000	0.91[EUR][1000 genomes]
rs10140801	0.87[CEU][hapmap];0.90[CHB][hapmap]
rs10140869	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs10141396	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10141483	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10141552	0.91[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10142448	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs10142547	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10142823	0.82[ASN][1000 genomes]
rs10144345	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10144418	0.87[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs10146637	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs10147765	0.91[EUR][1000 genomes]
rs10149420	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10150760	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs1045002	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs10467798	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1109170	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158034	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11625001	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap]
rs11625423	0.80[EUR][1000 genomes]
rs11626751	0.89[EUR][1000 genomes]
rs11628437	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11851169	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs13379169	0.84[ASN][1000 genomes]
rs1572611	0.83[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs17128440	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17674463	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs17674563	0.87[EUR][1000 genomes]
rs17740741	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs17741542	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17741831	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs1815580	0.88[EUR][1000 genomes]
rs1815581	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1972221	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2009291	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016931	0.91[EUR][1000 genomes]
rs2026633	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2075601	0.91[CEU][hapmap]
rs2075602	0.91[CEU][hapmap]
rs2075603	0.80[CEU][hapmap]
rs2182797	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2209808	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2340931	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs2341621	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2341622	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs28428911	0.91[EUR][1000 genomes]
rs28430823	0.91[EUR][1000 genomes]
rs28493647	0.91[EUR][1000 genomes]
rs28568813	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28612464	0.91[EUR][1000 genomes]
rs28631821	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28660594	0.91[EUR][1000 genomes]
rs28716725	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2880103	0.85[CHB][hapmap]
rs3742569	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs3783648	0.87[EUR][1000 genomes]
rs3783650	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783651	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs3783652	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs3818451	0.87[CEU][hapmap]
rs3825616	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]
rs4366639	0.80[EUR][1000 genomes]
rs4496026	0.80[EUR][1000 genomes]
rs4597235	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652	0.87[CEU][hapmap]
rs56270323	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61210954	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6573009	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap]
rs6573013	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6573014	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6573017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573020	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs66486619	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7144737	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs7145727	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7146748	0.84[ASN][1000 genomes]
rs7147136	0.87[EUR][1000 genomes]
rs7147247	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7148171	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7150234	0.82[ASN][1000 genomes]
rs7150763	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7151581	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs7152390	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7153110	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7154889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7155954	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7158768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7158791	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7159144	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7159808	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs7159824	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8004787	0.92[CEU][hapmap]
rs8005450	0.85[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs8006525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8008119	0.91[EUR][1000 genomes]
rs8013027	0.84[CEU][hapmap]
rs8013713	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs8014477	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8014540	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs8015211	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8021583	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs8022041	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8022225	0.86[ASN][1000 genomes]
rs8023197	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9323284	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs946059	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9919926	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs9919932	0.85[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11625968	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55779200-55817600	Weak transcription	Hela-S3	cervix
2	chr14:55779600-55801200	Weak transcription	Esophagus	oesophagus
3	chr14:55780200-55807800	Weak transcription	Thymus	Thymus
4	chr14:55780600-55806200	Weak transcription	HMEC	breast
5	chr14:55780800-55817200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr14:55782000-55817200	Weak transcription	HSMM	muscle
7	chr14:55784200-55801200	Weak transcription	Fetal Stomach	stomach
8	chr14:55786800-55803000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr14:55787200-55806600	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:55790400-55806800	Weak transcription	Aorta	Aorta
11	chr14:55791800-55817200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:55793000-55808600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:55794000-55801200	Weak transcription	Spleen	Spleen
14	chr14:55794000-55811800	Weak transcription	Brain Anterior Caudate	brain
15	chr14:55794400-55803000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:55795000-55806600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr14:55797600-55801200	Weak transcription	NHDF-Ad	bronchial
18	chr14:55797600-55803000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:55797800-55807800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr14:55798200-55817200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:55798800-55801800	Enhancers	Fetal Intestine Large	intestine
22	chr14:55798800-55802000	Enhancers	Small Intestine	intestine
23	chr14:55798800-55802200	Enhancers	Fetal Intestine Small	intestine
24	chr14:55798800-55802200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr14:55799000-55801200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr14:55799000-55801400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:55799000-55801600	Enhancers	Colon Smooth Muscle	Colon
28	chr14:55799000-55801800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr14:55799000-55802000	Enhancers	Primary B cells from peripheral blood	blood
30	chr14:55799000-55802000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr14:55799000-55802800	Enhancers	A549	lung
32	chr14:55799000-55804000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr14:55799200-55801400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr14:55799400-55801600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr14:55799400-55803600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:55799600-55801200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr14:55799600-55801400	Enhancers	Osteobl	bone
38	chr14:55799600-55801600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr14:55799600-55801600	Enhancers	NH-A	brain
40	chr14:55799600-55804400	Enhancers	Fetal Kidney	kidney
41	chr14:55799800-55801200	Enhancers	Primary hematopoietic stem cells	blood
42	chr14:55799800-55801200	Enhancers	Liver	Liver
43	chr14:55799800-55801200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr14:55799800-55801600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr14:55799800-55802200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr14:55799800-55804200	Weak transcription	Fetal Thymus	thymus
47	chr14:55800000-55801600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr14:55800000-55802200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr14:55800000-55802800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr14:55800000-55804400	Weak transcription	K562	blood

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