Variant report

Variant	rs4273727
Chromosome Location	chr6:109971581-109971582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10872051	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10872052	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1096139	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1096140	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1096142	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1102924	0.83[ASN][1000 genomes]
rs11153200	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153201	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11968485	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12204769	0.87[ASN][1000 genomes]
rs12211805	0.82[ASN][1000 genomes]
rs12211987	0.90[AMR][1000 genomes]
rs12215867	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12663674	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1406957	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1570013	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1575109	0.81[EUR][1000 genomes]
rs1885425	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1969710	0.80[EUR][1000 genomes]
rs2016207	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2076929	0.81[ASN][1000 genomes]
rs2145144	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2357130	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2884101	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4454170	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4946991	0.80[EUR][1000 genomes]
rs4946996	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4946999	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947003	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4947009	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62435982	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6568590	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6568593	0.80[AMR][1000 genomes]
rs6568594	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6568595	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6568596	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6900091	0.81[ASN][1000 genomes]
rs6917999	0.82[ASN][1000 genomes]
rs6918140	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6924269	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71541004	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs731879	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7356790	0.81[ASN][1000 genomes]
rs7450970	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740192	0.81[ASN][1000 genomes]
rs7744981	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7745406	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7745469	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7749910	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751458	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7753555	0.81[ASN][1000 genomes]
rs7761008	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7764783	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7765265	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829815	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829816	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829818	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853544	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9372221	0.81[EUR][1000 genomes]
rs9372222	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9374110	0.82[AMR][1000 genomes]
rs9374113	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9374114	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9384720	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9386826	0.81[EUR][1000 genomes]
rs9386833	0.81[ASN][1000 genomes]
rs9400307	0.85[ASN][1000 genomes]
rs9400310	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400312	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400313	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400315	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9400316	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480984	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480985	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480986	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9480987	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9480990	0.81[ASN][1000 genomes]
rs9480991	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9487160	0.81[ASN][1000 genomes]
rs9487172	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9487175	0.81[EUR][1000 genomes]
rs9487176	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9487178	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9487179	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9487180	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9487183	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs971432	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs971433	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9986423	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4273727	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4273727	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109933000-109985200	Weak transcription	Psoas Muscle	Psoas
2	chr6:109948000-109995000	Weak transcription	Brain Anterior Caudate	brain
3	chr6:109953800-109980800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:109959400-109975200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:109960000-109984000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
9	chr6:109961800-109981000	Weak transcription	Right Ventricle	heart
10	chr6:109962000-109983400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:109965200-109992200	Weak transcription	Fetal Brain Female	brain
12	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:109965600-109983200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:109965600-109983200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:109965600-109990800	Weak transcription	Primary B cells from cord blood	blood
16	chr6:109966000-109977000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:109966800-109991000	Weak transcription	Ovary	ovary
18	chr6:109966800-109993200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:109967200-109981800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:109967200-109986800	Weak transcription	Aorta	Aorta
21	chr6:109967200-109989800	Weak transcription	Gastric	stomach
22	chr6:109967200-109992600	Weak transcription	Left Ventricle	heart
23	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:109968400-109974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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