Variant report

Variant	rs1999908
Chromosome Location	chr6:45917819-45917820
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1001938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757345	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204333	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1204334	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1204335	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12192179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12198337	0.86[ASN][1000 genomes]
rs12211807	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1308732	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1890368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890369	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2396580	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734206	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777565	0.83[MEX][hapmap]
rs3777582	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.97[ASN][1000 genomes]
rs3777583	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777587	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777589	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777591	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777592	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236087	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4429946	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4563714	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4714895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6909306	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922752	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73460651	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1999908	CDC5L	cis	cerebellum	SCAN
rs1999908	GPR111	cis	parietal	SCAN
rs1999908	SUPT3H	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:45908000-45918600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:45908200-45918200	Weak transcription	Colonic Mucosa	Colon
4	chr6:45911000-45919200	Weak transcription	Small Intestine	intestine
5	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:45911200-45918000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:45911400-45919000	Weak transcription	Adipose Nuclei	Adipose
8	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:45912800-45928400	Weak transcription	Spleen	Spleen
10	chr6:45913400-45919000	Strong transcription	Fetal Intestine Small	intestine
11	chr6:45913800-45920000	Enhancers	Placenta	Placenta
12	chr6:45914200-45919200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:45914600-45918800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:45914600-45919400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:45915000-45919200	Weak transcription	Lung	lung
16	chr6:45915200-45919000	Weak transcription	Right Atrium	heart
17	chr6:45915400-45919000	Weak transcription	Fetal Heart	heart
18	chr6:45915800-45918800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:45915800-45919800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:45916200-45919400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:45916800-45919000	Weak transcription	Right Ventricle	heart
22	chr6:45917200-45918000	Enhancers	Hela-S3	cervix
23	chr6:45917200-45918800	Weak transcription	Fetal Intestine Large	intestine
24	chr6:45917200-45919000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:45917200-45919000	Weak transcription	Left Ventricle	heart
26	chr6:45917200-45919000	Weak transcription	Pancreas	Pancrea
27	chr6:45917200-45919000	Weak transcription	Psoas Muscle	Psoas
28	chr6:45917200-45919200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:45917200-45919200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:45917200-45924800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:45917400-45918800	Weak transcription	Fetal Kidney	kidney
32	chr6:45917400-45919000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:45917400-45919000	Weak transcription	HSMMtube	muscle
34	chr6:45917400-45919200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:45917800-45918000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr6:45917800-45918000	Enhancers	Rectal Mucosa Donor 31	rectum

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