Variant report

Variant	rs6568600
Chromosome Location	chr6:110039154-110039155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10872035	0.80[EUR][1000 genomes]
rs10872051	0.80[EUR][1000 genomes]
rs10872052	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1096139	0.81[EUR][1000 genomes]
rs1096142	0.81[EUR][1000 genomes]
rs11153194	0.84[EUR][1000 genomes]
rs11153200	0.96[CEU][hapmap]
rs11968485	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs12171561	0.91[ASN][1000 genomes]
rs12215867	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs12524352	0.95[CEU][hapmap]
rs12663674	0.80[EUR][1000 genomes]
rs1321327	0.96[CEU][hapmap]
rs1406957	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs1474959	0.96[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs1570013	0.96[CEU][hapmap]
rs1575108	0.86[EUR][1000 genomes]
rs1885425	0.82[EUR][1000 genomes]
rs2016207	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2093097	0.84[EUR][1000 genomes]
rs2145144	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2208210	0.85[EUR][1000 genomes]
rs2224550	0.86[MKK][hapmap]
rs2357128	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2357130	0.80[EUR][1000 genomes]
rs2357226	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884101	0.80[EUR][1000 genomes]
rs3823235	0.80[JPT][hapmap]
rs4454170	0.80[EUR][1000 genomes]
rs4523125	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs4946992	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs4946993	0.85[EUR][1000 genomes]
rs4946999	0.80[EUR][1000 genomes]
rs4947003	0.81[EUR][1000 genomes]
rs62435981	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6568580	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs6568590	0.81[EUR][1000 genomes]
rs6568595	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6568596	0.82[EUR][1000 genomes]
rs6568598	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6568602	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6568603	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916239	0.96[CEU][hapmap]
rs6918140	0.82[EUR][1000 genomes]
rs6922784	0.86[EUR][1000 genomes]
rs6924269	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6941360	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942171	0.81[TSI][hapmap]
rs731879	0.81[EUR][1000 genomes]
rs7450970	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7453835	0.96[CEU][hapmap]
rs7744981	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs7745469	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs7749910	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs7758697	0.91[ASN][1000 genomes]
rs7761008	0.96[CEU][hapmap]
rs7764783	0.81[EUR][1000 genomes]
rs7765265	0.80[EUR][1000 genomes]
rs829813	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs829814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs829815	0.81[EUR][1000 genomes]
rs829816	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs829818	0.82[EUR][1000 genomes]
rs9320304	0.96[CEU][hapmap]
rs9372221	0.96[CEU][hapmap]
rs9372222	0.96[CEU][hapmap]
rs9374095	0.96[CEU][hapmap]
rs9374097	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs9374108	0.96[CEU][hapmap]
rs9374110	0.96[CEU][hapmap]
rs9374113	0.81[EUR][1000 genomes]
rs9374114	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9374121	0.88[TSI][hapmap]
rs9384717	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs9384720	0.81[EUR][1000 genomes]
rs9386813	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs9386818	0.95[CEU][hapmap]
rs9386823	0.91[CEU][hapmap]
rs9386824	0.96[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap]
rs9386826	0.90[CEU][hapmap];0.81[YRI][hapmap]
rs9386839	0.96[ASN][1000 genomes]
rs9400288	0.80[EUR][1000 genomes]
rs9400310	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs9400312	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs9400313	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9400314	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9400315	0.81[EUR][1000 genomes]
rs9400316	0.96[CEU][hapmap];0.80[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs9400320	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480973	0.96[CEU][hapmap]
rs9480984	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs9480991	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs9481003	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9487171	0.96[CEU][hapmap]
rs9487172	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs9487175	0.96[CEU][hapmap]
rs9487176	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs9487180	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs9487202	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs971432	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs971433	0.81[EUR][1000 genomes]
rs9986423	0.81[EUR][1000 genomes]
rs9986507	0.96[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6568600	FIG4	cis	cerebellum	SCAN
rs6568600	FLJ42177	cis	multi-tissue	Pritchard
rs6568600	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
9	chr6:110027000-110040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:110027000-110052400	Weak transcription	Liver	Liver
11	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:110028000-110044000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:110033200-110041000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:110034200-110039400	Strong transcription	Primary T cells from cord blood	blood
18	chr6:110034400-110041600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:110034400-110042200	Weak transcription	NHLF	lung
20	chr6:110034400-110044400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
22	chr6:110034600-110041600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:110034600-110041800	Weak transcription	NHDF-Ad	bronchial
24	chr6:110034600-110046600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
26	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:110034800-110040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:110034800-110042000	Weak transcription	Lung	lung
29	chr6:110034800-110042400	Weak transcription	Brain Anterior Caudate	brain
30	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:110035000-110044000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
34	chr6:110035200-110039400	Weak transcription	Esophagus	oesophagus
35	chr6:110035200-110040400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:110035400-110039200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:110035400-110040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:110035400-110057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
43	chr6:110035600-110040200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:110035600-110040200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:110035600-110040600	Weak transcription	Gastric	stomach
46	chr6:110035600-110042000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:110035600-110044000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:110035600-110045000	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:110035600-110056400	Weak transcription	Ovary	ovary
50	chr6:110035600-110057000	Weak transcription	Pancreas	Pancrea

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