Variant report

Variant	rs829814
Chromosome Location	chr6:109995651-109995652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 196 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:189)

rs_ID	r²[population]
rs10457201	0.87[EUR][1000 genomes]
rs10872035	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10872041	0.85[EUR][1000 genomes]
rs10872047	0.85[EUR][1000 genomes]
rs10872051	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10872052	0.96[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1096139	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1096140	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1096142	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1102924	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11153193	0.85[EUR][1000 genomes]
rs11153194	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11153200	0.96[CEU][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs11153201	0.90[EUR][1000 genomes]
rs1115977	0.88[EUR][1000 genomes]
rs11966009	0.84[EUR][1000 genomes]
rs11968485	0.96[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12204769	0.86[EUR][1000 genomes]
rs12207793	0.85[EUR][1000 genomes]
rs12211805	0.83[EUR][1000 genomes]
rs12211987	0.82[EUR][1000 genomes]
rs12215867	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs12524352	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12663674	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1321327	0.96[CEU][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs1358759	0.84[EUR][1000 genomes]
rs1406957	0.96[CEU][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes]
rs1474959	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1570011	0.86[EUR][1000 genomes]
rs1570012	0.87[EUR][1000 genomes]
rs1570013	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1575108	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1575109	0.89[EUR][1000 genomes]
rs1590187	0.84[EUR][1000 genomes]
rs1885425	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1967725	0.88[EUR][1000 genomes]
rs1969710	0.87[EUR][1000 genomes]
rs1969711	0.88[EUR][1000 genomes]
rs1985123	0.84[EUR][1000 genomes]
rs1998812	0.85[EUR][1000 genomes]
rs2016207	0.96[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2064820	0.85[EUR][1000 genomes]
rs2093097	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2145144	0.96[CEU][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2208210	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357123	0.85[EUR][1000 genomes]
rs2357125	0.87[EUR][1000 genomes]
rs2357128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2357129	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357130	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2884101	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4454170	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4523125	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs4591898	0.83[EUR][1000 genomes]
rs4607459	0.81[EUR][1000 genomes]
rs4945835	0.85[EUR][1000 genomes]
rs4946986	0.85[EUR][1000 genomes]
rs4946987	0.85[EUR][1000 genomes]
rs4946989	0.87[EUR][1000 genomes]
rs4946991	0.86[EUR][1000 genomes]
rs4946992	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs4946993	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946996	0.90[EUR][1000 genomes]
rs4946999	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4947003	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4947009	0.85[EUR][1000 genomes]
rs62435981	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62435982	0.83[EUR][1000 genomes]
rs6568580	0.96[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs6568590	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568593	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6568594	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568595	0.96[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6568596	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568598	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6568600	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6568602	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6568603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs67715693	0.84[EUR][1000 genomes]
rs6916239	0.96[CEU][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes]
rs6918140	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6922784	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6924269	0.96[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6929823	0.86[EUR][1000 genomes]
rs6938499	0.81[EUR][1000 genomes]
rs6941360	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs71541004	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs731879	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7450970	0.96[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7453835	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs7454678	0.87[EUR][1000 genomes]
rs7454858	0.83[EUR][1000 genomes]
rs7744981	0.96[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7745406	0.82[EUR][1000 genomes]
rs7745469	0.96[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7749386	0.88[EUR][1000 genomes]
rs7749910	0.96[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7751458	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7752445	0.82[EUR][1000 genomes]
rs7754118	0.88[EUR][1000 genomes]
rs7754606	0.88[EUR][1000 genomes]
rs7761008	0.96[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs7764783	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7765265	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs829813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829815	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs829816	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs829818	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs853544	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9320294	0.83[EUR][1000 genomes]
rs9320295	0.84[EUR][1000 genomes]
rs9320296	0.84[EUR][1000 genomes]
rs9320299	0.86[EUR][1000 genomes]
rs9320304	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9320305	0.88[EUR][1000 genomes]
rs9372216	0.86[EUR][1000 genomes]
rs9372221	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9372222	0.96[CEU][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs9374092	0.83[EUR][1000 genomes]
rs9374095	0.96[CEU][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs9374097	0.96[CEU][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs9374098	0.82[EUR][1000 genomes]
rs9374099	0.85[EUR][1000 genomes]
rs9374108	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs9374110	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9374113	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9374114	0.96[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9384713	0.85[EUR][1000 genomes]
rs9384715	0.86[EUR][1000 genomes]
rs9384716	0.87[EUR][1000 genomes]
rs9384717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9384720	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9386812	0.85[EUR][1000 genomes]
rs9386813	0.96[CEU][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs9386816	0.85[EUR][1000 genomes]
rs9386818	0.96[CEU][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs9386820	0.80[EUR][1000 genomes]
rs9386823	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9386824	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9386825	0.88[EUR][1000 genomes]
rs9386826	0.91[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs9398204	0.83[EUR][1000 genomes]
rs9398206	0.87[EUR][1000 genomes]
rs9400288	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9400291	0.85[EUR][1000 genomes]
rs9400294	0.85[EUR][1000 genomes]
rs9400295	0.85[EUR][1000 genomes]
rs9400301	0.88[EUR][1000 genomes]
rs9400307	0.86[EUR][1000 genomes]
rs9400310	0.96[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9400312	0.96[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9400313	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9400314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9400315	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9400316	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9400320	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs942923	0.84[EUR][1000 genomes]
rs942924	0.85[EUR][1000 genomes]
rs9480973	0.96[CEU][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs9480974	0.85[EUR][1000 genomes]
rs9480976	0.85[EUR][1000 genomes]
rs9480982	0.88[EUR][1000 genomes]
rs9480984	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs9480985	0.90[EUR][1000 genomes]
rs9480986	0.91[EUR][1000 genomes]
rs9480987	0.86[EUR][1000 genomes]
rs9480991	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9481003	0.89[CHB][hapmap]
rs9487141	0.85[EUR][1000 genomes]
rs9487148	0.85[EUR][1000 genomes]
rs9487152	0.82[EUR][1000 genomes]
rs9487153	0.81[EUR][1000 genomes]
rs9487156	0.87[EUR][1000 genomes]
rs9487160	0.88[EUR][1000 genomes]
rs9487164	0.87[EUR][1000 genomes]
rs9487169	0.82[EUR][1000 genomes]
rs9487170	0.88[EUR][1000 genomes]
rs9487171	0.96[CEU][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs9487172	0.96[CEU][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs9487175	0.96[CEU][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs9487176	0.96[CEU][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs9487178	0.90[EUR][1000 genomes]
rs9487179	0.86[EUR][1000 genomes]
rs9487180	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9487183	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs971432	0.96[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs971433	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9986423	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9986507	0.96[CEU][hapmap];0.88[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
rs829814	SMPD2	cis	Whole Blood	GTEx
rs829814	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 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	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:109979600-110000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:109980200-109999800	Weak transcription	Pancreas	Pancrea
8	chr6:109980600-109998600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
10	chr6:109983600-110000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:109985200-110000800	Weak transcription	Spleen	Spleen
12	chr6:109987200-109998400	Weak transcription	Aorta	Aorta
13	chr6:109988200-109998600	Weak transcription	Fetal Heart	heart
14	chr6:109988600-109998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:109989200-109998200	Weak transcription	Small Intestine	intestine
16	chr6:109989400-109997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:109989400-110011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:109990000-110010600	Weak transcription	Fetal Intestine Small	intestine
19	chr6:109991000-109999600	Weak transcription	Primary T cells from cord blood	blood
20	chr6:109991400-110007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:109991400-110010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:109992000-110011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:109992400-110011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:109993400-109996200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:109993800-109998000	Weak transcription	Primary B cells from cord blood	blood
26	chr6:109994000-110000000	Weak transcription	Left Ventricle	heart
27	chr6:109994400-110001000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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