Variant report

Variant	rs2932777
Chromosome Location	chr5:68525027-68525028
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	chr5:68523954..68526904-chr5:68529417..68531065,2	MCF-7	breast:
2	chr5:68524400..68526328-chr5:68527569..68529446,2	K562	blood:

Variant related genes	Relation type
ENSG00000134058	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs100192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940209	0.81[ASN][1000 genomes]
rs11742461	0.90[ASN][1000 genomes]
rs11744596	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745578	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs12659146	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175606	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs151589	0.83[ASN][1000 genomes]
rs163442	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163444	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs164386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164388	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164389	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164715	0.83[ASN][1000 genomes]
rs1683831	0.92[ASN][1000 genomes]
rs184747	0.83[ASN][1000 genomes]
rs2002825	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130757	0.81[ASN][1000 genomes]
rs2171148	0.81[ASN][1000 genomes]
rs2172056	0.81[ASN][1000 genomes]
rs2242351	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291519	0.81[ASN][1000 genomes]
rs2291520	0.81[ASN][1000 genomes]
rs239591	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450230	0.84[ASN][1000 genomes]
rs2450246	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2637128	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637129	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28506805	0.92[ASN][1000 genomes]
rs28576332	0.90[ASN][1000 genomes]
rs28693971	0.90[ASN][1000 genomes]
rs2913707	0.83[ASN][1000 genomes]
rs2930944	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930945	0.85[ASN][1000 genomes]
rs2930946	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930949	0.81[ASN][1000 genomes]
rs2930951	0.81[ASN][1000 genomes]
rs2932770	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932772	0.85[ASN][1000 genomes]
rs2932773	0.85[ASN][1000 genomes]
rs2932775	0.85[ASN][1000 genomes]
rs2932776	0.85[ASN][1000 genomes]
rs2932778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932780	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932782	0.80[ASN][1000 genomes]
rs2932783	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972358	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972361	0.81[ASN][1000 genomes]
rs2972366	0.81[ASN][1000 genomes]
rs2972373	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972374	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972381	0.81[ASN][1000 genomes]
rs2972386	0.81[ASN][1000 genomes]
rs2972387	0.81[ASN][1000 genomes]
rs2972388	0.80[ASN][1000 genomes]
rs2972390	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34845020	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350093	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350094	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350095	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350099	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350107	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.83[ASN][1000 genomes]
rs350119	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350120	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350123	0.85[ASN][1000 genomes]
rs350124	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350125	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351424	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs352626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353656	0.82[ASN][1000 genomes]
rs375285	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376768	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379434	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386640	0.83[ASN][1000 genomes]
rs389686	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs389938	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390169	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395122	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419902	0.83[ASN][1000 genomes]
rs4266362	0.82[ASN][1000 genomes]
rs437665	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476125	0.92[ASN][1000 genomes]
rs4976159	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4976188	0.91[ASN][1000 genomes]
rs648489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651076	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs676879	0.81[ASN][1000 genomes]
rs6862253	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7719040	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	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
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2932777	MRPS36	cis	lymphoblastoid	seeQTL
rs2932777	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2932777	MRPS36	cis	multi-tissue	Pritchard
rs2932777	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68514200-68530200	Weak transcription	Small Intestine	intestine
2	chr5:68514200-68530200	Weak transcription	Spleen	Spleen
3	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
8	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
9	chr5:68514400-68530200	Weak transcription	Gastric	stomach
10	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
11	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
14	chr5:68515200-68529800	Weak transcription	Fetal Brain Female	brain
15	chr5:68515200-68529800	Weak transcription	NHLF	lung
16	chr5:68515200-68530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:68515200-68530000	Weak transcription	Fetal Brain Male	brain
18	chr5:68515200-68530000	Weak transcription	Fetal Kidney	kidney
19	chr5:68515200-68530000	Weak transcription	Fetal Lung	lung
20	chr5:68515400-68526000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:68515400-68529400	Weak transcription	Fetal Heart	heart
22	chr5:68515400-68529800	Weak transcription	Brain Anterior Caudate	brain
23	chr5:68515400-68529800	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:68515400-68529800	Weak transcription	Hela-S3	cervix
25	chr5:68515400-68530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:68515400-68530000	Weak transcription	Right Ventricle	heart
27	chr5:68515600-68530000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:68515600-68530000	Weak transcription	Brain Substantia Nigra	brain
29	chr5:68515800-68530000	Weak transcription	Brain Angular Gyrus	brain
30	chr5:68520200-68526400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:68520400-68525600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:68520400-68526400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:68520400-68526600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:68520400-68528200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:68520800-68529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr5:68520800-68530200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:68521000-68526400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:68521000-68526400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:68521400-68526400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:68521600-68526000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:68521600-68526000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:68521800-68526400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:68521800-68526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:68521800-68530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:68522000-68526200	Strong transcription	Fetal Intestine Large	intestine
46	chr5:68522200-68526400	Strong transcription	Fetal Thymus	thymus
47	chr5:68522800-68526000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:68522800-68526200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:68522800-68526400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:68522800-68526400	Strong transcription	Rectal Mucosa Donor 29	rectum

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