Variant report

Variant	rs6862253
Chromosome Location	chr5:68581750-68581751
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	chr5:68580179..68583024-chr5:68584330..68585895,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs100192	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs10940209	0.83[ASN][1000 genomes]
rs10940210	0.85[ASN][1000 genomes]
rs11742461	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744596	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11745578	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520485	0.81[ASN][1000 genomes]
rs12652119	0.84[ASN][1000 genomes]
rs12659146	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13175606	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs163442	0.84[ASN][1000 genomes]
rs163443	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs163444	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs164386	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs164388	0.85[ASN][1000 genomes]
rs164389	0.83[ASN][1000 genomes]
rs164390	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs1683831	0.81[ASN][1000 genomes]
rs2002825	0.89[ASN][1000 genomes]
rs2130757	0.83[ASN][1000 genomes]
rs2171148	0.83[ASN][1000 genomes]
rs2172056	0.83[ASN][1000 genomes]
rs2242351	0.89[ASN][1000 genomes]
rs2291519	0.83[ASN][1000 genomes]
rs2291520	0.83[ASN][1000 genomes]
rs239591	0.82[ASN][1000 genomes]
rs2450246	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2637128	0.90[ASN][1000 genomes]
rs2637129	0.86[ASN][1000 genomes]
rs28506805	0.81[ASN][1000 genomes]
rs28576332	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28602964	0.84[ASN][1000 genomes]
rs28693971	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2930944	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930946	0.89[ASN][1000 genomes]
rs2930949	0.83[ASN][1000 genomes]
rs2930951	0.83[ASN][1000 genomes]
rs2932770	0.89[ASN][1000 genomes]
rs2932771	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932777	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932778	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932780	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932782	0.83[ASN][1000 genomes]
rs2932783	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972358	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972361	0.83[ASN][1000 genomes]
rs2972366	0.83[ASN][1000 genomes]
rs2972373	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972374	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972381	0.83[ASN][1000 genomes]
rs2972386	0.83[ASN][1000 genomes]
rs2972387	0.83[ASN][1000 genomes]
rs2972388	0.83[ASN][1000 genomes]
rs2972390	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34845020	0.87[ASN][1000 genomes]
rs350093	0.83[ASN][1000 genomes]
rs350095	0.88[ASN][1000 genomes]
rs350099	0.84[ASN][1000 genomes]
rs350105	0.83[ASN][1000 genomes]
rs350107	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs350119	0.85[ASN][1000 genomes]
rs350120	0.89[CEU][hapmap];0.87[ASN][1000 genomes]
rs350124	0.89[ASN][1000 genomes]
rs350125	0.88[ASN][1000 genomes]
rs351424	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs352626	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs375285	0.87[ASN][1000 genomes]
rs376768	0.85[ASN][1000 genomes]
rs379434	0.85[ASN][1000 genomes]
rs389686	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs389938	0.85[ASN][1000 genomes]
rs390169	0.80[ASN][1000 genomes]
rs3934528	0.85[ASN][1000 genomes]
rs395122	0.85[ASN][1000 genomes]
rs4077460	0.85[ASN][1000 genomes]
rs4266362	0.80[ASN][1000 genomes]
rs4362903	0.85[ASN][1000 genomes]
rs437665	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4421064	0.85[ASN][1000 genomes]
rs444305	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4541612	0.84[ASN][1000 genomes]
rs476125	0.81[ASN][1000 genomes]
rs4976159	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4976188	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62373164	0.85[ASN][1000 genomes]
rs648489	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs651076	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6865178	0.81[ASN][1000 genomes]
rs6876783	0.85[ASN][1000 genomes]
rs693725	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7719040	0.87[ASN][1000 genomes]
rs875459	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6862253	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs6862253	CCDC125	cis	Muscle Skeletal	GTEx
rs6862253	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 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	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
7	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:68563000-68585200	Strong transcription	Liver	Liver
12	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
13	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:68569400-68582000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:68573000-68587800	Weak transcription	Hela-S3	cervix
18	chr5:68573000-68590600	Weak transcription	HUVEC	blood vessel
19	chr5:68573200-68585600	Strong transcription	Fetal Intestine Small	intestine
20	chr5:68574000-68585000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:68575600-68584200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
24	chr5:68576000-68583800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:68576000-68584200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
27	chr5:68576200-68584200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:68576200-68590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:68576400-68583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:68576400-68583800	Weak transcription	Fetal Lung	lung
33	chr5:68576400-68584000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:68576400-68591000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:68576400-68593000	Weak transcription	HMEC	breast
36	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
38	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:68576600-68582800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr5:68576600-68583600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:68576600-68583800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:68576600-68595400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
44	chr5:68577000-68591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:68577200-68584000	Weak transcription	Lung	lung
46	chr5:68577200-68601400	Weak transcription	Aorta	Aorta
47	chr5:68577400-68583600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:68577400-68583800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr5:68577400-68584200	Weak transcription	Gastric	stomach
50	chr5:68577400-68588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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