Variant report

Variant	rs6568603
Chromosome Location	chr6:110054486-110054487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10872052	0.96[CEU][hapmap]
rs11153194	0.82[EUR][1000 genomes]
rs11153200	0.96[CEU][hapmap]
rs11968485	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs12171561	0.91[ASN][1000 genomes]
rs12215867	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs12524352	0.95[CEU][hapmap]
rs1321327	0.96[CEU][hapmap]
rs1406957	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs1474959	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[TSI][hapmap]
rs1570013	0.96[CEU][hapmap]
rs1575108	0.84[EUR][1000 genomes]
rs2016207	0.96[CEU][hapmap]
rs2093097	0.82[EUR][1000 genomes]
rs2145144	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs2208210	0.83[EUR][1000 genomes]
rs2224550	0.86[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap]
rs2357128	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2357226	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823235	0.80[JPT][hapmap]
rs4523125	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs4946992	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs4946993	0.83[EUR][1000 genomes]
rs62435981	0.85[EUR][1000 genomes]
rs6568583	0.80[TSI][hapmap]
rs6568591	0.80[TSI][hapmap]
rs6568595	0.96[CEU][hapmap]
rs6568598	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6568600	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]
rs6568602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916239	0.96[CEU][hapmap]
rs6922784	0.84[EUR][1000 genomes]
rs6924269	0.96[CEU][hapmap]
rs6941360	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942171	0.83[TSI][hapmap]
rs7450970	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs7453835	0.96[CEU][hapmap]
rs7744981	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs7745469	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs7749910	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs7758697	0.91[ASN][1000 genomes]
rs7761008	0.96[CEU][hapmap]
rs829813	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs829814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs829816	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs911022	0.80[TSI][hapmap]
rs9320304	0.96[CEU][hapmap]
rs9372221	0.96[CEU][hapmap]
rs9372222	0.96[CEU][hapmap]
rs9374095	0.96[CEU][hapmap]
rs9374097	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9374108	0.96[CEU][hapmap]
rs9374110	0.96[CEU][hapmap]
rs9374114	0.96[CEU][hapmap]
rs9374121	0.85[MEX][hapmap];0.90[TSI][hapmap]
rs9384717	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs9386813	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9386818	0.95[CEU][hapmap]
rs9386823	0.91[CEU][hapmap]
rs9386824	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs9386826	0.90[CEU][hapmap]
rs9386839	0.94[ASN][1000 genomes]
rs9400310	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9400312	0.96[CEU][hapmap]
rs9400313	0.95[CEU][hapmap]
rs9400314	0.86[EUR][1000 genomes]
rs9400316	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs9400320	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9480973	0.96[CEU][hapmap]
rs9480984	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9480991	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9481003	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9487171	0.96[CEU][hapmap]
rs9487172	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs9487175	0.96[CEU][hapmap]
rs9487176	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs9487180	0.96[CEU][hapmap]
rs9487202	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs971432	0.96[CEU][hapmap]
rs9986507	0.82[ASW][hapmap];0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6568603	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs6568603	FIG4	cis	cerebellum	SCAN

Chromatin state (count:94 , 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	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
14	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
15	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
19	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:110035400-110057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:110035600-110056400	Weak transcription	Ovary	ovary
25	chr6:110035600-110057000	Weak transcription	Pancreas	Pancrea
26	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
27	chr6:110035800-110057000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:110035800-110065000	Weak transcription	HSMM	muscle
29	chr6:110036200-110056200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr6:110036600-110057000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
32	chr6:110037200-110056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:110037200-110056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:110037600-110057000	Weak transcription	Psoas Muscle	Psoas
35	chr6:110038000-110056400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:110038000-110057000	Weak transcription	Fetal Intestine Large	intestine
37	chr6:110038400-110056400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:110039000-110054600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:110039000-110056400	Weak transcription	Placenta	Placenta
40	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:110039200-110057000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:110039200-110058800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:110039600-110056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:110039600-110057000	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:110039800-110062000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:110040400-110056400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:110040800-110062000	Weak transcription	Thymus	Thymus
48	chr6:110041000-110056000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:110041000-110057000	Weak transcription	Esophagus	oesophagus
50	chr6:110041000-110064800	Weak transcription	Gastric	stomach

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