Variant report

Variant	rs4947016
Chromosome Location	chr6:110062098-110062099
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10457203	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153213	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11153215	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153216	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752791	0.81[EUR][1000 genomes]
rs11754340	0.81[EUR][1000 genomes]
rs11755641	0.82[EUR][1000 genomes]
rs12190372	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12191353	0.84[EUR][1000 genomes]
rs12192268	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12192776	0.87[EUR][1000 genomes]
rs12193719	0.82[EUR][1000 genomes]
rs12194157	0.87[EUR][1000 genomes]
rs12197838	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197950	0.88[EUR][1000 genomes]
rs12201356	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12201444	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203993	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12204548	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12205140	0.86[EUR][1000 genomes]
rs12205485	0.83[EUR][1000 genomes]
rs12208018	0.80[EUR][1000 genomes]
rs12210706	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12215077	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12528392	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528781	0.85[EUR][1000 genomes]
rs13198852	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13199109	0.88[EUR][1000 genomes]
rs13199135	0.82[EUR][1000 genomes]
rs13201430	0.80[EUR][1000 genomes]
rs1322124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1960325	0.81[EUR][1000 genomes]
rs1980591	0.84[EUR][1000 genomes]
rs2025147	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2025148	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2273752	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799845	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3799849	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3899233	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4141930	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4490694	0.81[EUR][1000 genomes]
rs4945833	0.81[EUR][1000 genomes]
rs6568592	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6911700	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71541003	0.90[EUR][1000 genomes]
rs729888	0.87[EUR][1000 genomes]
rs7341297	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7451512	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767525	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4947016	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs4947016	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4947016	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs4947016	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
6	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
9	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
10	chr6:110035800-110065000	Weak transcription	HSMM	muscle
11	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
12	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:110041000-110064800	Weak transcription	Gastric	stomach
14	chr6:110041000-110065000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:110041000-110065000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
20	chr6:110045800-110064800	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:110047000-110067200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
23	chr6:110047600-110068800	Weak transcription	Dnd41	blood
24	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
25	chr6:110050400-110065800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
27	chr6:110054200-110063200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:110055000-110064800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:110055400-110065000	Weak transcription	Osteobl	bone
30	chr6:110055800-110063000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:110056000-110066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:110056400-110062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:110056400-110063400	Strong transcription	Primary T cells from cord blood	blood
34	chr6:110056600-110063000	Strong transcription	Primary hematopoietic stem cells	blood
35	chr6:110056800-110067400	Weak transcription	Fetal Lung	lung
36	chr6:110057000-110062800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:110057200-110064400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:110057200-110064800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
40	chr6:110057400-110064800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:110057400-110064800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:110057400-110065000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
44	chr6:110057600-110062200	Weak transcription	Brain Substantia Nigra	brain
45	chr6:110057600-110065000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:110057800-110064800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:110057800-110064800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:110057800-110065000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:110057800-110065200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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