Variant report

Variant	rs4946998
Chromosome Location	chr6:109961505-109961506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 173 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10457201	0.82[EUR][1000 genomes]
rs10872051	0.84[EUR][1000 genomes]
rs10872052	0.84[EUR][1000 genomes]
rs1096136	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096139	0.82[EUR][1000 genomes]
rs1096140	0.80[EUR][1000 genomes]
rs1096142	0.82[EUR][1000 genomes]
rs11153193	0.80[EUR][1000 genomes]
rs11153200	0.84[EUR][1000 genomes]
rs11153201	0.85[EUR][1000 genomes]
rs1115977	0.83[EUR][1000 genomes]
rs11753828	0.87[EUR][1000 genomes]
rs11754263	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968485	0.83[EUR][1000 genomes]
rs12200787	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12204769	0.82[EUR][1000 genomes]
rs12215867	0.84[EUR][1000 genomes]
rs12524352	0.83[EUR][1000 genomes]
rs12663674	0.82[EUR][1000 genomes]
rs1321327	0.82[EUR][1000 genomes]
rs1406957	0.85[EUR][1000 genomes]
rs1474959	0.83[EUR][1000 genomes]
rs1570011	0.81[EUR][1000 genomes]
rs1570012	0.82[EUR][1000 genomes]
rs1570013	0.84[EUR][1000 genomes]
rs1575109	0.84[EUR][1000 genomes]
rs17540056	0.87[EUR][1000 genomes]
rs1885425	0.81[EUR][1000 genomes]
rs1925921	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967725	0.83[EUR][1000 genomes]
rs1969710	0.83[EUR][1000 genomes]
rs1969711	0.83[EUR][1000 genomes]
rs2016207	0.83[EUR][1000 genomes]
rs2064822	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357125	0.82[EUR][1000 genomes]
rs2357127	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357130	0.84[EUR][1000 genomes]
rs2884101	0.84[EUR][1000 genomes]
rs4296926	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4454170	0.84[EUR][1000 genomes]
rs4523125	0.83[EUR][1000 genomes]
rs4946982	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946989	0.82[EUR][1000 genomes]
rs4946991	0.82[EUR][1000 genomes]
rs4946992	0.83[EUR][1000 genomes]
rs4946995	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946996	0.85[EUR][1000 genomes]
rs4946997	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946999	0.84[EUR][1000 genomes]
rs4947002	0.82[EUR][1000 genomes]
rs4947003	0.83[EUR][1000 genomes]
rs4947004	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56264193	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61170920	0.84[EUR][1000 genomes]
rs62437563	0.87[EUR][1000 genomes]
rs6568579	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568582	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568583	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568586	0.81[EUR][1000 genomes]
rs6568590	0.83[EUR][1000 genomes]
rs6568591	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568594	0.81[EUR][1000 genomes]
rs6568595	0.83[EUR][1000 genomes]
rs6568596	0.81[EUR][1000 genomes]
rs6568601	0.87[EUR][1000 genomes]
rs6900133	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6912368	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6917300	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918140	0.81[EUR][1000 genomes]
rs6921303	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.81[EUR][1000 genomes]
rs6924436	0.89[EUR][1000 genomes]
rs6925886	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929823	0.81[EUR][1000 genomes]
rs6931630	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6938741	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6942171	0.87[EUR][1000 genomes]
rs731879	0.83[EUR][1000 genomes]
rs7450970	0.83[EUR][1000 genomes]
rs7453835	0.83[EUR][1000 genomes]
rs7454678	0.83[EUR][1000 genomes]
rs7744981	0.84[EUR][1000 genomes]
rs7745469	0.84[EUR][1000 genomes]
rs7749386	0.83[EUR][1000 genomes]
rs7749910	0.84[EUR][1000 genomes]
rs7751458	0.81[EUR][1000 genomes]
rs7754118	0.83[EUR][1000 genomes]
rs7754606	0.83[EUR][1000 genomes]
rs7761008	0.85[EUR][1000 genomes]
rs7764783	0.83[EUR][1000 genomes]
rs7765265	0.84[EUR][1000 genomes]
rs7771729	0.89[EUR][1000 genomes]
rs7772109	0.89[EUR][1000 genomes]
rs7773915	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7775420	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829815	0.83[EUR][1000 genomes]
rs829816	0.83[EUR][1000 genomes]
rs829817	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829818	0.82[EUR][1000 genomes]
rs853544	0.81[EUR][1000 genomes]
rs911022	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320299	0.81[EUR][1000 genomes]
rs9320300	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320304	0.83[EUR][1000 genomes]
rs9320305	0.83[EUR][1000 genomes]
rs9372216	0.81[EUR][1000 genomes]
rs9372220	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.84[EUR][1000 genomes]
rs9372222	0.83[EUR][1000 genomes]
rs9374096	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374108	0.83[EUR][1000 genomes]
rs9374113	0.83[EUR][1000 genomes]
rs9374114	0.83[EUR][1000 genomes]
rs9384715	0.81[EUR][1000 genomes]
rs9384716	0.82[EUR][1000 genomes]
rs9384720	0.83[EUR][1000 genomes]
rs9386814	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386816	0.80[EUR][1000 genomes]
rs9386818	0.83[EUR][1000 genomes]
rs9386823	0.83[EUR][1000 genomes]
rs9386824	0.83[EUR][1000 genomes]
rs9386825	0.83[EUR][1000 genomes]
rs9386826	0.84[EUR][1000 genomes]
rs9398206	0.82[EUR][1000 genomes]
rs9400289	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400300	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400301	0.83[EUR][1000 genomes]
rs9400307	0.82[EUR][1000 genomes]
rs9400310	0.84[EUR][1000 genomes]
rs9400312	0.83[EUR][1000 genomes]
rs9400313	0.83[EUR][1000 genomes]
rs9400315	0.83[EUR][1000 genomes]
rs9400316	0.83[EUR][1000 genomes]
rs9480982	0.83[EUR][1000 genomes]
rs9480984	0.84[EUR][1000 genomes]
rs9480985	0.85[EUR][1000 genomes]
rs9480986	0.84[EUR][1000 genomes]
rs9480991	0.83[EUR][1000 genomes]
rs9487156	0.82[EUR][1000 genomes]
rs9487160	0.83[EUR][1000 genomes]
rs9487164	0.82[EUR][1000 genomes]
rs9487170	0.83[EUR][1000 genomes]
rs9487171	0.83[EUR][1000 genomes]
rs9487172	0.84[EUR][1000 genomes]
rs9487175	0.84[EUR][1000 genomes]
rs9487176	0.84[EUR][1000 genomes]
rs9487178	0.85[EUR][1000 genomes]
rs9487179	0.82[EUR][1000 genomes]
rs9487180	0.84[EUR][1000 genomes]
rs9487183	0.81[EUR][1000 genomes]
rs971432	0.83[EUR][1000 genomes]
rs971433	0.83[EUR][1000 genomes]
rs9968792	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9986423	0.83[EUR][1000 genomes]
rs9986507	0.83[EUR][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
rs4946998	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4946998	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109928000-109966400	Weak transcription	Pancreas	Pancrea
2	chr6:109933000-109962800	Weak transcription	Left Ventricle	heart
3	chr6:109933000-109966400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:109933000-109985200	Weak transcription	Psoas Muscle	Psoas
5	chr6:109945400-109966400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:109947200-109966800	Weak transcription	Gastric	stomach
7	chr6:109948000-109995000	Weak transcription	Brain Anterior Caudate	brain
8	chr6:109953200-109963000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:109953200-109966200	Weak transcription	Fetal Intestine Small	intestine
10	chr6:109953800-109963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:109953800-109966400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:109953800-109980800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:109954000-109963000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:109954000-109965200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:109959400-109975200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:109960000-109984000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:109961200-109961600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr6:109961200-109961600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:109961200-109961600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:109961200-109961600	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr6:109961200-109961600	ZNF genes & repeats	Aorta	Aorta
23	chr6:109961200-109961600	ZNF genes & repeats	Liver	Liver
24	chr6:109961200-109961600	ZNF genes & repeats	Brain Angular Gyrus	brain
25	chr6:109961200-109961600	ZNF genes & repeats	Brain Substantia Nigra	brain
26	chr6:109961200-109961600	ZNF genes & repeats	Fetal Brain Female	brain
27	chr6:109961200-109961600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
28	chr6:109961200-109961600	ZNF genes & repeats	Thymus	Thymus
29	chr6:109961200-109961600	ZNF genes & repeats	Spleen	Spleen
30	chr6:109961200-109961800	ZNF genes & repeats	Lung	lung
31	chr6:109961200-109961800	ZNF genes & repeats	Right Ventricle	heart
32	chr6:109961200-109962000	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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