Variant report

Variant	rs10798598
Chromosome Location	chr1:171668697-171668698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171667939..171671943-chr1:171675100..171678672,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10798599	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798603	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913488	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10913508	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913530	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913559	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10913586	0.86[EUR][1000 genomes]
rs11583530	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11805692	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11806314	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12045452	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12096984	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12120152	0.93[EUR][1000 genomes]
rs12139610	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073484	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227229	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4342884	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4468194	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425400	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6659539	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6665581	0.93[EUR][1000 genomes]
rs6668623	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672082	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6673782	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674468	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674688	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674774	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6682452	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6685742	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688447	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs763225	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9660076	0.80[AMR][1000 genomes]
rs999685	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10798598	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664600-171674400	Weak transcription	Primary T cells from cord blood	blood
3	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:171665000-171669000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
6	chr1:171665400-171674600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:171666000-171669000	Strong transcription	Aorta	Aorta
10	chr1:171666000-171674200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
14	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
15	chr1:171666200-171670800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:171666200-171676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:171666200-171682600	Weak transcription	Lung	lung
18	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
19	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
20	chr1:171666400-171673000	Weak transcription	Primary B cells from cord blood	blood
21	chr1:171666600-171676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:171666600-171686200	Weak transcription	Gastric	stomach
24	chr1:171666800-171669800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:171666800-171670000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:171666800-171671800	Weak transcription	Liver	Liver
27	chr1:171666800-171673600	Weak transcription	HSMM	muscle
28	chr1:171666800-171674200	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:171666800-171674200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:171666800-171675600	Weak transcription	Colonic Mucosa	Colon
31	chr1:171666800-171679200	Weak transcription	NH-A	brain
32	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:171667000-171669600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:171667000-171670400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:171667000-171672600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:171667000-171672800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:171667000-171675800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:171667000-171676600	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:171667000-171676800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:171667000-171685000	Weak transcription	Osteobl	bone
45	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
46	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
47	chr1:171667200-171670600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:171667200-171672800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:171667400-171669000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:171667400-171670600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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