Variant report

Variant	rs499600
Chromosome Location	chr1:46039077-46039078
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45266030..45268033-chr1:46037084..46039498,2	K562	blood:
2	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
3	chr1:46031645..46033631-chr1:46038341..46040543,2	MCF-7	breast:
4	chr1:45985335..45987528-chr1:46038480..46041554,5	K562	blood:
5	chr1:45965940..45967492-chr1:46038830..46041668,2	K562	blood:
6	chr1:45973063..45975262-chr1:46038700..46040345,2	MCF-7	breast:
7	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
8	chr1:46023197..46024863-chr1:46038353..46040089,2	K562	blood:
9	chr1:46037943..46043170-chr1:46048057..46052696,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132763	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10430105	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs10430123	0.81[CHB][hapmap];0.84[YRI][hapmap]
rs10430124	0.81[CHB][hapmap];0.84[YRI][hapmap]
rs10749856	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs10789467	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs10789470	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs10789471	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap]
rs1084086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs10890333	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs10890334	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs10890335	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs10890336	0.80[CHB][hapmap];0.89[YRI][hapmap]
rs10890341	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs11211145	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs11211146	1.00[YRI][hapmap]
rs11211147	1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap]
rs11211149	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11211152	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs11211157	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs11211160	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs11211161	0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs11211163	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs11211166	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs11211168	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs11211169	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs11211171	0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs11211173	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap]
rs11211177	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1135812	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs12023439	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12024590	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs12037459	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12043945	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs12049027	0.80[CHB][hapmap]
rs12091503	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs1250	0.82[CHB][hapmap]
rs1547924	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs1547925	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs1972410	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs2050376	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs2152078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs2230658	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs2230659	0.86[CHB][hapmap];0.95[YRI][hapmap]
rs2253862	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs2275085	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs2275086	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs28370457	0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap]
rs28375469	0.95[CHB][hapmap];0.84[YRI][hapmap]
rs28550303	0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs28719889	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap]
rs28890893	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap]
rs2991978	0.87[ASN][1000 genomes]
rs2991979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs2991986	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs2991987	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs2991988	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs2991989	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs3013597	0.82[CHB][hapmap]
rs3014210	0.82[CHB][hapmap]
rs3014213	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3014235	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs3014237	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs3014239	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs3014241	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs3014242	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs3014245	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs3790585	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811436	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs4439382	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs4468203	0.81[CHB][hapmap]
rs4559551	0.81[CHB][hapmap];0.95[YRI][hapmap]
rs4564187	0.82[CHB][hapmap];0.95[YRI][hapmap]
rs4607935	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs4609469	0.83[CHB][hapmap];0.95[YRI][hapmap]
rs4660313	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs4660880	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4660882	0.82[CHB][hapmap]
rs512083	0.84[ASN][1000 genomes]
rs514595	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518216	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs659437	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6658700	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs666720	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6694889	0.95[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs6697821	0.81[CHB][hapmap];0.84[YRI][hapmap]
rs6703748	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap]
rs9429172	1.00[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs499600	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46032600-46049000	Weak transcription	Right Atrium	heart
2	chr1:46033000-46048800	Weak transcription	Fetal Brain Male	brain
3	chr1:46034200-46039800	Weak transcription	Small Intestine	intestine
4	chr1:46034200-46048800	Weak transcription	Stomach Mucosa	stomach
5	chr1:46035000-46041000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:46035000-46042600	Weak transcription	HMEC	breast
7	chr1:46035200-46039600	Weak transcription	Fetal Heart	heart
8	chr1:46035400-46039200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:46035400-46039600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:46035400-46048800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:46035600-46048000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:46035600-46048800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:46035800-46039600	Weak transcription	Aorta	Aorta
14	chr1:46035800-46039600	Weak transcription	Colonic Mucosa	Colon
15	chr1:46035800-46039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:46035800-46040000	Weak transcription	Left Ventricle	heart
17	chr1:46035800-46041000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:46035800-46041800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:46035800-46048800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:46035800-46048800	Weak transcription	Hela-S3	cervix
21	chr1:46036000-46039600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:46036200-46047600	Weak transcription	Primary B cells from cord blood	blood
23	chr1:46036200-46048800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:46036400-46039200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:46036400-46039200	Weak transcription	Ovary	ovary
26	chr1:46036400-46039400	Weak transcription	Right Ventricle	heart
27	chr1:46036400-46039600	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:46036400-46039800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:46036400-46039800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:46036400-46039800	Weak transcription	Fetal Stomach	stomach
31	chr1:46036400-46041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:46036400-46048000	Weak transcription	Spleen	Spleen
33	chr1:46036400-46048600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:46036400-46048800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:46036400-46048800	Weak transcription	Brain Germinal Matrix	brain
36	chr1:46036400-46049200	Weak transcription	Gastric	stomach
37	chr1:46036600-46039600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:46036600-46039800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:46036600-46039800	Weak transcription	HUVEC	blood vessel
40	chr1:46036600-46040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:46036600-46040200	Weak transcription	HSMMtube	muscle
42	chr1:46036600-46040200	Weak transcription	NHEK	skin
43	chr1:46036600-46047400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:46036600-46048200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:46036600-46048600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:46036600-46048600	Weak transcription	Lung	lung
47	chr1:46036600-46048800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:46036600-46048800	Weak transcription	Brain Anterior Caudate	brain
49	chr1:46036600-46048800	Weak transcription	Fetal Kidney	kidney
50	chr1:46036600-46048800	Weak transcription	Fetal Lung	lung

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