Variant report

Variant	rs1128998
Chromosome Location	chr6:133092046-133092047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10457591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457593	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457595	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457596	0.85[CEU][hapmap]
rs10484628	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10484629	1.00[CHB][hapmap]
rs11154698	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191058	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193474	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12194625	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12194802	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12195249	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12196336	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199381	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12200848	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12201540	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12201769	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202407	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12204693	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12204740	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12204863	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12207011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12209144	1.00[JPT][hapmap]
rs12211425	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12211701	1.00[CHB][hapmap]
rs12212934	0.85[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12215084	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12215088	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12215486	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1467403	1.00[CHB][hapmap]
rs1467404	1.00[CHB][hapmap]
rs17061751	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2143387	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294761	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28693848	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28706652	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3778173	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778175	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55708537	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56170227	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58265543	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60062075	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425110	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425113	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425114	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425132	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425133	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62425137	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6569847	1.00[CHB][hapmap]
rs6912936	1.00[CHB][hapmap]
rs7738071	1.00[CHB][hapmap]
rs7738400	1.00[CHB][hapmap]
rs7758703	1.00[CHB][hapmap]
rs7761365	1.00[CHB][hapmap]
rs7765224	1.00[CHB][hapmap]
rs7770081	1.00[CHB][hapmap]
rs9321367	1.00[CHB][hapmap]
rs9375919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389033	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493435	1.00[CHB][hapmap]
rs9493436	1.00[CHB][hapmap]
rs9493437	1.00[CHB][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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1128998	C6orf192	Cis_1M	lymphoblastoid	RTeQTL
rs1128998	C6orf192	cis	multi-tissue	Pritchard
rs1128998	C6orf192	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133061400-133098000	Weak transcription	Spleen	Spleen
2	chr6:133065000-133098000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:133081400-133096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:133083600-133099000	Weak transcription	Left Ventricle	heart
5	chr6:133083800-133118200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:133084800-133097000	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:133085000-133109000	Weak transcription	GM12878-XiMat	blood
8	chr6:133085000-133114600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:133085000-133119000	Weak transcription	Thymus	Thymus
10	chr6:133085200-133112200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:133085200-133119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:133085400-133114400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:133085600-133098800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:133085600-133099800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:133085600-133118800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:133085800-133093200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:133085800-133100000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:133085800-133100000	Weak transcription	Aorta	Aorta
19	chr6:133085800-133119000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:133086000-133093600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:133086000-133112800	Weak transcription	Hela-S3	cervix
22	chr6:133086000-133113800	Weak transcription	NHEK	skin
23	chr6:133086000-133118800	Weak transcription	Fetal Kidney	kidney
24	chr6:133086200-133107800	Weak transcription	Osteobl	bone
25	chr6:133086400-133096200	Weak transcription	HMEC	breast
26	chr6:133086400-133097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:133086400-133110200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:133086600-133099400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:133086600-133103400	Weak transcription	Brain Anterior Caudate	brain
30	chr6:133088200-133111200	Weak transcription	HUVEC	blood vessel
31	chr6:133088600-133098000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:133088600-133099200	Weak transcription	Fetal Brain Female	brain
33	chr6:133088600-133114600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:133089400-133094600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:133089400-133100000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:133089400-133104400	Weak transcription	Brain Germinal Matrix	brain
37	chr6:133089400-133110400	Weak transcription	Colonic Mucosa	Colon
38	chr6:133089400-133111800	Weak transcription	Lung	lung
39	chr6:133089400-133119400	Weak transcription	Gastric	stomach
40	chr6:133089600-133093800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:133089600-133096800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:133089600-133097200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:133089600-133099000	Weak transcription	Fetal Thymus	thymus
44	chr6:133089600-133099800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:133089600-133099800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:133089600-133100000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:133089600-133100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:133089600-133100000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:133089600-133102000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:133089600-133111400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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