Variant report

Variant	rs829817
Chromosome Location	chr6:109998285-109998286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109996616..109999325-chr6:110011516..110013836,2	K562	blood:

Variant related genes	Relation type
ENSG00000155085	Chromatin interaction
ENSG00000112367	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10872051	0.84[EUR][1000 genomes]
rs10872052	0.84[EUR][1000 genomes]
rs1096136	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[EUR][1000 genomes]
rs11153201	0.83[EUR][1000 genomes]
rs1115977	0.81[EUR][1000 genomes]
rs11753828	0.89[EUR][1000 genomes]
rs11754263	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968485	0.85[EUR][1000 genomes]
rs12200787	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215867	0.81[EUR][1000 genomes]
rs12524352	0.81[EUR][1000 genomes]
rs12663674	0.84[EUR][1000 genomes]
rs1406957	0.83[EUR][1000 genomes]
rs1474959	0.81[EUR][1000 genomes]
rs1570013	0.82[EUR][1000 genomes]
rs1575109	0.82[EUR][1000 genomes]
rs17540056	0.89[EUR][1000 genomes]
rs1885425	0.83[EUR][1000 genomes]
rs1925921	0.81[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	0.85[EUR][1000 genomes]
rs2064822	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145144	0.82[EUR][1000 genomes]
rs2357127	0.86[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	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4454170	0.84[EUR][1000 genomes]
rs4523125	0.81[EUR][1000 genomes]
rs4946982	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946992	0.81[EUR][1000 genomes]
rs4946995	0.89[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	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946998	0.92[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	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56125306	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56264193	0.88[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]
rs6568579	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6568582	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568583	0.86[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	0.96[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	0.85[EUR][1000 genomes]
rs6568596	0.83[EUR][1000 genomes]
rs6568601	0.89[EUR][1000 genomes]
rs6900133	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900187	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911851	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6912368	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6917300	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918140	0.83[EUR][1000 genomes]
rs6921303	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924269	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	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932774	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938741	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6942171	0.89[EUR][1000 genomes]
rs71541004	0.81[EUR][1000 genomes]
rs731879	0.85[EUR][1000 genomes]
rs7450970	0.85[EUR][1000 genomes]
rs7453835	0.81[EUR][1000 genomes]
rs7454678	0.80[EUR][1000 genomes]
rs7744981	0.84[EUR][1000 genomes]
rs7745469	0.84[EUR][1000 genomes]
rs7749386	0.81[EUR][1000 genomes]
rs7749910	0.84[EUR][1000 genomes]
rs7751458	0.83[EUR][1000 genomes]
rs7754118	0.81[EUR][1000 genomes]
rs7754606	0.81[EUR][1000 genomes]
rs7761008	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	0.86[EUR][1000 genomes]
rs7775420	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829815	0.85[EUR][1000 genomes]
rs829816	0.85[EUR][1000 genomes]
rs829818	0.84[EUR][1000 genomes]
rs853544	0.83[EUR][1000 genomes]
rs911022	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320290	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320300	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320304	0.81[EUR][1000 genomes]
rs9320305	0.81[EUR][1000 genomes]
rs9372220	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372221	0.82[EUR][1000 genomes]
rs9372222	0.80[EUR][1000 genomes]
rs9374096	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374108	0.81[EUR][1000 genomes]
rs9374113	0.85[EUR][1000 genomes]
rs9374114	0.85[EUR][1000 genomes]
rs9384720	0.85[EUR][1000 genomes]
rs9386814	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386818	0.81[EUR][1000 genomes]
rs9386823	0.81[EUR][1000 genomes]
rs9386824	0.81[EUR][1000 genomes]
rs9386825	0.81[EUR][1000 genomes]
rs9386826	0.82[EUR][1000 genomes]
rs9400289	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400300	0.84[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	0.84[EUR][1000 genomes]
rs9400312	0.85[EUR][1000 genomes]
rs9400313	0.85[EUR][1000 genomes]
rs9400315	0.85[EUR][1000 genomes]
rs9400316	0.85[EUR][1000 genomes]
rs9480982	0.81[EUR][1000 genomes]
rs9480984	0.81[EUR][1000 genomes]
rs9480985	0.83[EUR][1000 genomes]
rs9480986	0.84[EUR][1000 genomes]
rs9480991	0.85[EUR][1000 genomes]
rs9487160	0.81[EUR][1000 genomes]
rs9487170	0.81[EUR][1000 genomes]
rs9487171	0.81[EUR][1000 genomes]
rs9487172	0.82[EUR][1000 genomes]
rs9487175	0.82[EUR][1000 genomes]
rs9487176	0.81[EUR][1000 genomes]
rs9487178	0.83[EUR][1000 genomes]
rs9487180	0.84[EUR][1000 genomes]
rs9487183	0.83[EUR][1000 genomes]
rs971432	0.85[EUR][1000 genomes]
rs971433	0.85[EUR][1000 genomes]
rs9968792	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9986423	0.85[EUR][1000 genomes]
rs9986507	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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
rs829817	SMPD2	cis	Whole Blood	GTEx
rs829817	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
3	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
5	chr6:109979600-110000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:109980200-109999800	Weak transcription	Pancreas	Pancrea
7	chr6:109980600-109998600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
9	chr6:109983600-110000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:109985200-110000800	Weak transcription	Spleen	Spleen
11	chr6:109987200-109998400	Weak transcription	Aorta	Aorta
12	chr6:109988200-109998600	Weak transcription	Fetal Heart	heart
13	chr6:109989400-110011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:109990000-110010600	Weak transcription	Fetal Intestine Small	intestine
15	chr6:109991000-109999600	Weak transcription	Primary T cells from cord blood	blood
16	chr6:109991400-110007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:109991400-110010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:109992000-110011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:109992400-110011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:109994000-110000000	Weak transcription	Left Ventricle	heart
21	chr6:109994400-110001000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:109997800-109998400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:109998000-109998400	ZNF genes & repeats	Primary B cells from cord blood	blood

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