Variant report

Variant	rs6866993
Chromosome Location	chr5:68587900-68587901
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	chr5:68585755..68588228-chr5:68664183..68666734,2	MCF-7	breast:
2	chr5:68529509..68531449-chr5:68587302..68589559,2	K562	blood:

Variant related genes	Relation type
ENSG00000134058	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs100192	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10045526	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10063969	0.82[AMR][1000 genomes]
rs10471774	0.82[AMR][1000 genomes]
rs10940209	0.92[ASN][1000 genomes]
rs10940210	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940212	0.89[ASN][1000 genomes]
rs10940214	0.83[ASN][1000 genomes]
rs10940216	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742461	0.86[ASN][1000 genomes]
rs11745578	0.86[ASN][1000 genomes]
rs11748974	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513817	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13175606	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13362324	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs151589	0.92[ASN][1000 genomes]
rs163443	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs163444	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs164386	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs164390	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs164715	0.92[ASN][1000 genomes]
rs1650779	0.86[ASN][1000 genomes]
rs171211	0.80[AMR][1000 genomes]
rs171212	0.85[ASN][1000 genomes]
rs184747	0.92[ASN][1000 genomes]
rs2130757	0.92[ASN][1000 genomes]
rs2171148	0.92[ASN][1000 genomes]
rs2172056	0.92[ASN][1000 genomes]
rs2291519	0.92[ASN][1000 genomes]
rs2291520	0.92[ASN][1000 genomes]
rs2450230	0.93[ASN][1000 genomes]
rs2450246	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28576332	0.86[ASN][1000 genomes]
rs28602964	0.93[ASN][1000 genomes]
rs28693971	0.86[ASN][1000 genomes]
rs2930945	0.94[ASN][1000 genomes]
rs2930949	0.92[ASN][1000 genomes]
rs2930951	0.92[ASN][1000 genomes]
rs2932767	0.87[ASN][1000 genomes]
rs2932772	0.94[ASN][1000 genomes]
rs2932773	0.94[ASN][1000 genomes]
rs2932775	0.94[ASN][1000 genomes]
rs2932776	0.94[ASN][1000 genomes]
rs2932778	0.81[ASN][1000 genomes]
rs2932782	0.92[ASN][1000 genomes]
rs2972361	0.92[ASN][1000 genomes]
rs2972366	0.92[ASN][1000 genomes]
rs2972377	0.81[ASN][1000 genomes]
rs2972378	0.81[ASN][1000 genomes]
rs2972381	0.92[ASN][1000 genomes]
rs2972386	0.92[ASN][1000 genomes]
rs2972387	0.92[ASN][1000 genomes]
rs2972388	0.92[ASN][1000 genomes]
rs34935424	0.92[ASN][1000 genomes]
rs350107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs350109	0.93[ASN][1000 genomes]
rs350115	0.92[ASN][1000 genomes]
rs350116	0.88[ASN][1000 genomes]
rs350122	0.85[ASN][1000 genomes]
rs350123	0.94[ASN][1000 genomes]
rs350125	0.80[ASN][1000 genomes]
rs351424	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs352626	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs353656	0.90[ASN][1000 genomes]
rs379106	0.88[ASN][1000 genomes]
rs386640	0.92[ASN][1000 genomes]
rs3890705	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs389686	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3934528	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077460	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs419902	0.92[ASN][1000 genomes]
rs4266362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4362903	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs437665	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs4421064	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs444305	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4541612	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4629549	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488498	0.83[ASN][1000 genomes]
rs4976159	0.85[ASN][1000 genomes]
rs4976188	0.83[ASN][1000 genomes]
rs4976189	0.92[ASN][1000 genomes]
rs4976190	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603029	0.83[ASN][1000 genomes]
rs62373164	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373181	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62373187	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6450029	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648489	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs651076	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs676879	0.90[ASN][1000 genomes]
rs6873869	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6876783	0.94[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7733556	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875459	0.91[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6866993	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs6866993	KENAE	cis	multi-tissue	Pritchard
rs6866993	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs6866993	MRPS36	cis	lymphoblastoid	seeQTL
rs6866993	CCDC125	cis	lung	GTEx
rs6866993	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
3	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
6	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:68573000-68590600	Weak transcription	HUVEC	blood vessel
10	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
12	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
13	chr5:68576200-68590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:68576400-68591000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:68576400-68593000	Weak transcription	HMEC	breast
18	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
20	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:68576600-68595400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
23	chr5:68577000-68591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:68577200-68601400	Weak transcription	Aorta	Aorta
25	chr5:68577400-68588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:68577400-68590400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:68577400-68594400	Weak transcription	Esophagus	oesophagus
28	chr5:68577400-68605200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:68577400-68607800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
31	chr5:68577600-68590600	Weak transcription	K562	blood
32	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:68577600-68627400	Weak transcription	NHEK	skin
34	chr5:68577800-68588000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:68577800-68626600	Weak transcription	A549	lung
36	chr5:68578200-68590800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:68578800-68590600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:68579000-68590600	Weak transcription	NH-A	brain
39	chr5:68579000-68590600	Weak transcription	Osteobl	bone
40	chr5:68579000-68603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:68580600-68594200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:68581600-68588200	Weak transcription	Ovary	ovary
43	chr5:68581600-68590400	Weak transcription	Thymus	Thymus
44	chr5:68581600-68590800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr5:68581600-68601200	Weak transcription	Fetal Thymus	thymus
46	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:68581800-68588200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr5:68581800-68588200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr5:68581800-68589000	Weak transcription	Placenta	Placenta
50	chr5:68581800-68589600	Weak transcription	Primary T cells fromperipheralblood	blood

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