Variant report

Variant	rs4947006
Chromosome Location	chr6:109981433-109981434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs10872051	0.84[EUR][1000 genomes]
rs10872052	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1096136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096138	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1096139	0.85[EUR][1000 genomes]
rs1096140	0.82[EUR][1000 genomes]
rs1096142	0.85[EUR][1000 genomes]
rs1102924	0.81[EUR][1000 genomes]
rs11153200	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11153201	0.83[EUR][1000 genomes]
rs1115977	0.81[EUR][1000 genomes]
rs11751112	0.82[YRI][hapmap]
rs11753828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs11754263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757485	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs11968485	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12200787	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215867	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12524352	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12663674	0.84[EUR][1000 genomes]
rs1321327	0.81[CEU][hapmap]
rs1406957	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1474959	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1570013	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1575109	0.82[EUR][1000 genomes]
rs17540056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17612758	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap]
rs17612996	0.83[YRI][hapmap]
rs1885425	0.83[EUR][1000 genomes]
rs1925921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967725	0.81[EUR][1000 genomes]
rs1969710	0.80[EUR][1000 genomes]
rs1969711	0.81[EUR][1000 genomes]
rs2016207	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2064822	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2232448	0.83[YRI][hapmap]
rs2357127	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357130	0.84[EUR][1000 genomes]
rs2884101	0.84[EUR][1000 genomes]
rs4296926	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4454170	0.84[EUR][1000 genomes]
rs4523125	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4946982	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946992	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4946995	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946996	0.83[EUR][1000 genomes]
rs4946997	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946999	0.84[EUR][1000 genomes]
rs4947002	0.82[EUR][1000 genomes]
rs4947003	0.85[EUR][1000 genomes]
rs4947004	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56264193	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61170920	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62437563	0.89[EUR][1000 genomes]
rs6568578	1.00[CHB][hapmap]
rs6568579	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6568582	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568590	0.85[EUR][1000 genomes]
rs6568591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6568594	0.83[EUR][1000 genomes]
rs6568595	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6568596	0.83[EUR][1000 genomes]
rs6568601	0.89[EUR][1000 genomes]
rs6900133	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6912368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6916239	0.85[CEU][hapmap]
rs6917300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918140	0.83[EUR][1000 genomes]
rs6921303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs6924436	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6925886	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938741	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6942171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs71541004	0.81[EUR][1000 genomes]
rs731879	0.85[EUR][1000 genomes]
rs7450970	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7453835	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7454678	0.80[EUR][1000 genomes]
rs7744981	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7745469	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7749386	0.81[EUR][1000 genomes]
rs7749910	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7751458	0.83[EUR][1000 genomes]
rs7754118	0.81[EUR][1000 genomes]
rs7754606	0.81[EUR][1000 genomes]
rs7756284	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs7761008	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7764783	0.85[EUR][1000 genomes]
rs7765265	0.84[EUR][1000 genomes]
rs7771729	0.89[EUR][1000 genomes]
rs7772109	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7773915	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7775420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829815	0.85[EUR][1000 genomes]
rs829816	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs829817	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829818	0.84[EUR][1000 genomes]
rs853544	0.83[EUR][1000 genomes]
rs911022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	1.00[CEU][hapmap];1.00[CHB][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]
rs9320290	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320300	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320303	1.00[CEU][hapmap]
rs9320304	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9320305	0.81[EUR][1000 genomes]
rs9372220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs9372222	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9374095	0.81[CEU][hapmap]
rs9374096	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374097	0.81[CEU][hapmap]
rs9374108	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9374110	0.80[CEU][hapmap]
rs9374113	0.85[EUR][1000 genomes]
rs9374114	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9384720	0.85[EUR][1000 genomes]
rs9386813	0.81[CEU][hapmap]
rs9386814	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386818	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9386823	0.81[EUR][1000 genomes]
rs9386824	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9386825	0.81[EUR][1000 genomes]
rs9386826	0.82[EUR][1000 genomes]
rs9400289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400300	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400301	0.81[EUR][1000 genomes]
rs9400310	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs9400312	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs9400313	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs9400315	0.85[EUR][1000 genomes]
rs9400316	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9480973	0.81[CEU][hapmap]
rs9480982	0.81[EUR][1000 genomes]
rs9480984	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9480985	0.83[EUR][1000 genomes]
rs9480986	0.84[EUR][1000 genomes]
rs9480991	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9487160	0.81[EUR][1000 genomes]
rs9487170	0.81[EUR][1000 genomes]
rs9487171	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs9487172	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs9487175	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9487176	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9487178	0.83[EUR][1000 genomes]
rs9487180	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs9487183	0.83[EUR][1000 genomes]
rs971432	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs971433	0.85[EUR][1000 genomes]
rs9968792	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9986423	0.85[EUR][1000 genomes]
rs9986507	0.81[CEU][hapmap];0.81[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
rs4947006	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4947006	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:40 , 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	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:109960000-109984000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
7	chr6:109962000-109983400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:109965200-109992200	Weak transcription	Fetal Brain Female	brain
9	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:109965600-109983200	Weak transcription	Brain Substantia Nigra	brain
11	chr6:109965600-109983200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:109965600-109990800	Weak transcription	Primary B cells from cord blood	blood
13	chr6:109966800-109991000	Weak transcription	Ovary	ovary
14	chr6:109966800-109993200	Weak transcription	Adipose Nuclei	Adipose
15	chr6:109967200-109981800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:109967200-109986800	Weak transcription	Aorta	Aorta
17	chr6:109967200-109989800	Weak transcription	Gastric	stomach
18	chr6:109967200-109992600	Weak transcription	Left Ventricle	heart
19	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:109972400-109992200	Weak transcription	Liver	Liver
21	chr6:109974200-109992400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:109976000-109992800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:109976200-109981600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
25	chr6:109978200-109990800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:109978400-109991200	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:109978600-109990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:109978600-109991000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:109979600-109992600	Weak transcription	HSMMtube	muscle
30	chr6:109979600-110000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:109980000-109982800	Weak transcription	Lung	lung
32	chr6:109980200-109999800	Weak transcription	Pancreas	Pancrea
33	chr6:109980600-109998600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
35	chr6:109981200-109983800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:109981200-109983800	Enhancers	NHEK	skin
37	chr6:109981200-109992600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:109981400-109983600	Enhancers	HMEC	breast
39	chr6:109981400-109983800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:109981400-109984800	Enhancers	HUVEC	blood vessel

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