Variant report

Variant	rs7752445
Chromosome Location	chr6:109989217-109989218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10457201	0.84[EUR][1000 genomes]
rs10872041	0.82[EUR][1000 genomes]
rs10872047	0.82[EUR][1000 genomes]
rs10872051	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10872052	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1096139	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1096140	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1096142	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1102924	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11153193	0.82[EUR][1000 genomes]
rs11153200	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11153201	0.87[EUR][1000 genomes]
rs1115977	0.85[EUR][1000 genomes]
rs11966009	0.81[EUR][1000 genomes]
rs11968485	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12204769	0.83[EUR][1000 genomes]
rs12207793	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12211805	0.82[EUR][1000 genomes]
rs12211987	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12215867	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12524352	0.85[EUR][1000 genomes]
rs12663674	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1321327	0.84[EUR][1000 genomes]
rs1358759	0.81[EUR][1000 genomes]
rs1406957	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1474959	0.85[EUR][1000 genomes]
rs1570011	0.83[EUR][1000 genomes]
rs1570012	0.84[EUR][1000 genomes]
rs1570013	0.86[EUR][1000 genomes]
rs1575109	0.86[EUR][1000 genomes]
rs1590187	0.81[EUR][1000 genomes]
rs1885425	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967725	0.85[EUR][1000 genomes]
rs1969710	0.84[EUR][1000 genomes]
rs1969711	0.85[EUR][1000 genomes]
rs1985123	0.81[EUR][1000 genomes]
rs1998812	0.82[EUR][1000 genomes]
rs2016207	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2064820	0.82[EUR][1000 genomes]
rs2145144	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2357123	0.82[EUR][1000 genomes]
rs2357125	0.84[EUR][1000 genomes]
rs2357130	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2884101	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4454170	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4523125	0.85[EUR][1000 genomes]
rs4591898	0.80[EUR][1000 genomes]
rs4946986	0.82[EUR][1000 genomes]
rs4946987	0.82[EUR][1000 genomes]
rs4946989	0.84[EUR][1000 genomes]
rs4946991	0.83[EUR][1000 genomes]
rs4946992	0.85[EUR][1000 genomes]
rs4946996	0.87[EUR][1000 genomes]
rs4946999	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4947003	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4947009	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62435981	0.81[EUR][1000 genomes]
rs62435982	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6568580	0.81[EUR][1000 genomes]
rs6568590	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6568593	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6568594	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6568595	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6568596	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67715693	0.81[EUR][1000 genomes]
rs6916239	0.82[EUR][1000 genomes]
rs6918140	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6924269	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6929823	0.83[EUR][1000 genomes]
rs71541004	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs731879	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7450970	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7453835	0.85[EUR][1000 genomes]
rs7454678	0.84[EUR][1000 genomes]
rs7454858	0.80[EUR][1000 genomes]
rs7744981	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7745406	0.82[EUR][1000 genomes]
rs7745469	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7749386	0.85[EUR][1000 genomes]
rs7749910	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7751458	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7754118	0.85[EUR][1000 genomes]
rs7754606	0.85[EUR][1000 genomes]
rs7761008	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7764783	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7765265	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs829813	0.80[EUR][1000 genomes]
rs829814	0.82[EUR][1000 genomes]
rs829815	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829816	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829818	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs853544	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9320294	0.80[EUR][1000 genomes]
rs9320295	0.81[EUR][1000 genomes]
rs9320296	0.81[EUR][1000 genomes]
rs9320299	0.83[EUR][1000 genomes]
rs9320304	0.85[EUR][1000 genomes]
rs9320305	0.85[EUR][1000 genomes]
rs9372216	0.83[EUR][1000 genomes]
rs9372221	0.86[EUR][1000 genomes]
rs9372222	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9374092	0.80[EUR][1000 genomes]
rs9374095	0.82[EUR][1000 genomes]
rs9374097	0.82[EUR][1000 genomes]
rs9374099	0.82[EUR][1000 genomes]
rs9374108	0.85[EUR][1000 genomes]
rs9374113	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9374114	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9384713	0.82[EUR][1000 genomes]
rs9384715	0.83[EUR][1000 genomes]
rs9384716	0.84[EUR][1000 genomes]
rs9384720	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9386812	0.82[EUR][1000 genomes]
rs9386813	0.82[EUR][1000 genomes]
rs9386816	0.84[EUR][1000 genomes]
rs9386818	0.85[EUR][1000 genomes]
rs9386823	0.85[EUR][1000 genomes]
rs9386824	0.85[EUR][1000 genomes]
rs9386825	0.85[EUR][1000 genomes]
rs9386826	0.86[EUR][1000 genomes]
rs9398204	0.80[EUR][1000 genomes]
rs9398206	0.84[EUR][1000 genomes]
rs9400291	0.82[EUR][1000 genomes]
rs9400294	0.82[EUR][1000 genomes]
rs9400295	0.82[EUR][1000 genomes]
rs9400301	0.85[EUR][1000 genomes]
rs9400307	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9400310	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9400312	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9400313	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9400314	0.82[EUR][1000 genomes]
rs9400315	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9400316	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs942923	0.81[EUR][1000 genomes]
rs942924	0.82[EUR][1000 genomes]
rs9480973	0.82[EUR][1000 genomes]
rs9480974	0.82[EUR][1000 genomes]
rs9480976	0.82[EUR][1000 genomes]
rs9480982	0.85[EUR][1000 genomes]
rs9480984	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9480985	0.87[EUR][1000 genomes]
rs9480986	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9480987	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9480991	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9487141	0.82[EUR][1000 genomes]
rs9487148	0.82[EUR][1000 genomes]
rs9487156	0.84[EUR][1000 genomes]
rs9487160	0.85[EUR][1000 genomes]
rs9487164	0.86[EUR][1000 genomes]
rs9487170	0.85[EUR][1000 genomes]
rs9487171	0.85[EUR][1000 genomes]
rs9487172	0.86[EUR][1000 genomes]
rs9487175	0.86[EUR][1000 genomes]
rs9487176	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9487178	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9487179	0.83[EUR][1000 genomes]
rs9487180	0.88[EUR][1000 genomes]
rs9487183	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs971432	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs971433	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9986423	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9986507	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	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
rs7752445	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs7752445	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109948000-109995000	Weak transcription	Brain Anterior Caudate	brain
2	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
5	chr6:109965200-109992200	Weak transcription	Fetal Brain Female	brain
6	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:109965600-109990800	Weak transcription	Primary B cells from cord blood	blood
8	chr6:109966800-109991000	Weak transcription	Ovary	ovary
9	chr6:109966800-109993200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:109967200-109989800	Weak transcription	Gastric	stomach
11	chr6:109967200-109992600	Weak transcription	Left Ventricle	heart
12	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:109972400-109992200	Weak transcription	Liver	Liver
14	chr6:109974200-109992400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:109976000-109992800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
17	chr6:109978200-109990800	Weak transcription	Primary T cells from cord blood	blood
18	chr6:109978400-109991200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:109978600-109990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:109978600-109991000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:109979600-109992600	Weak transcription	HSMMtube	muscle
22	chr6:109979600-110000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:109980200-109999800	Weak transcription	Pancreas	Pancrea
24	chr6:109980600-109998600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
26	chr6:109981200-109992600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:109982600-109992800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:109983600-110000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:109984200-109992600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:109985200-110000800	Weak transcription	Spleen	Spleen
31	chr6:109985800-109991000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:109986800-109994600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:109987200-109998400	Weak transcription	Aorta	Aorta
34	chr6:109988200-109998600	Weak transcription	Fetal Heart	heart
35	chr6:109988600-109998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:109989200-109995400	Weak transcription	Fetal Stomach	stomach
37	chr6:109989200-109998200	Weak transcription	Small Intestine	intestine

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