Variant report

Variant	rs4421064
Chromosome Location	chr5:68578428-68578429
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	chr5:68577265..68579159-chr5:68664266..68665815,2	K562	blood:
2	chr5:68572340..68574718-chr5:68576377..68579078,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF9-3	chr5:68577172-68578861	NONHSAT101908

Variant related genes	Relation type
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs100192	0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs10063757	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10940209	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940210	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940212	0.83[ASN][1000 genomes]
rs10940216	0.83[ASN][1000 genomes]
rs11742461	0.80[ASN][1000 genomes]
rs11745578	0.80[ASN][1000 genomes]
rs11748974	0.91[ASN][1000 genomes]
rs12513817	0.85[EUR][1000 genomes]
rs13175606	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs13362324	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs151589	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs163443	0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs163444	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs164386	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs164390	0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs164709	0.82[EUR][1000 genomes]
rs164715	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1650779	0.86[ASN][1000 genomes]
rs171212	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs184747	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1976103	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2130757	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171148	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172056	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242350	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2291519	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291520	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2450230	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2450246	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs28576332	0.80[ASN][1000 genomes]
rs28602964	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28693971	0.80[ASN][1000 genomes]
rs28768211	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930945	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2930949	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930951	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932767	0.84[ASN][1000 genomes]
rs2932772	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932773	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932775	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932776	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932778	0.80[ASN][1000 genomes]
rs2932780	0.84[ASN][1000 genomes]
rs2932782	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932783	0.83[ASN][1000 genomes]
rs2972361	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972366	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972378	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972381	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972386	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972387	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972388	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34893396	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34935424	0.86[ASN][1000 genomes]
rs350104	0.88[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs350106	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs350107	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350109	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350115	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350116	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350122	0.84[ASN][1000 genomes]
rs350123	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs352626	0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap]
rs35308484	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs353656	0.89[ASN][1000 genomes]
rs379106	0.87[ASN][1000 genomes]
rs386640	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3890705	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs389686	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3934528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4077460	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419902	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4266362	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4362903	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437665	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs444305	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4541612	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4629549	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs488498	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4976159	0.80[ASN][1000 genomes]
rs4976188	0.82[ASN][1000 genomes]
rs4976189	0.86[ASN][1000 genomes]
rs4976190	0.80[ASN][1000 genomes]
rs603029	0.82[ASN][1000 genomes]
rs62373164	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450026	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6450027	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6450029	0.86[ASN][1000 genomes]
rs648489	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs651076	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs676012	0.88[CEU][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs676879	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6862253	0.85[ASN][1000 genomes]
rs6866993	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873869	0.86[ASN][1000 genomes]
rs6876783	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693725	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733556	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	0.90[CHB][hapmap];0.84[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
rs4421064	CCDC125	cis	Muscle Skeletal	GTEx
rs4421064	MRPS36	cis	lymphoblastoid	seeQTL
rs4421064	MRPS36	cis	multi-tissue	Pritchard
rs4421064	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs4421064	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs4421064	CCDC125	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
4	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:68553000-68581400	Weak transcription	Psoas Muscle	Psoas
10	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
11	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:68559200-68581200	Weak transcription	Fetal Kidney	kidney
14	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:68562600-68578800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:68563000-68585200	Strong transcription	Liver	Liver
18	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
19	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr5:68569400-68582000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:68570800-68578800	Strong transcription	Adipose Nuclei	Adipose
24	chr5:68571600-68579000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:68571600-68579800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr5:68571600-68581600	Strong transcription	Fetal Thymus	thymus
27	chr5:68573000-68587800	Weak transcription	Hela-S3	cervix
28	chr5:68573000-68590600	Weak transcription	HUVEC	blood vessel
29	chr5:68573200-68585600	Strong transcription	Fetal Intestine Small	intestine
30	chr5:68573800-68580400	Weak transcription	NHDF-Ad	bronchial
31	chr5:68574000-68585000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:68574800-68581200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:68575000-68579000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr5:68575400-68578800	Strong transcription	Primary B cells from cord blood	blood
35	chr5:68575400-68581600	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:68575600-68584200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
39	chr5:68576000-68583800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:68576000-68584200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
42	chr5:68576200-68584200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:68576200-68590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:68576400-68581200	Weak transcription	GM12878-XiMat	blood
47	chr5:68576400-68581400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:68576400-68581600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:68576400-68581600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:68576400-68583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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