Variant report

Variant	rs3790585
Chromosome Location	chr1:46023356-46023357
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
2	chr1:46023197..46024863-chr1:46038353..46040089,2	K562	blood:
3	chr1:45985097..45987613-chr1:46022518..46025124,4	MCF-7	breast:
4	chr1:46013953..46018760-chr1:46019151..46024741,9	K562	blood:
5	chr1:45982318..45989250-chr1:46023024..46029715,13	K562	blood:
6	chr1:46021695..46023515-chr1:46048571..46051513,2	K562	blood:
7	chr1:46021617..46024409-chr1:46027059..46029406,2	K562	blood:
8	chr1:46015251..46018245-chr1:46018589..46025048,8	MCF-7	breast:
9	chr1:46013953..46019415-chr1:46020167..46024741,10	K562	blood:
10	chr1:45983804..45987826-chr1:46021822..46025099,5	K562	blood:

No data

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

Extended variants
information (count: 90 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10430105	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs10749856	0.82[YRI][hapmap]
rs10789467	0.82[YRI][hapmap]
rs10789470	0.80[YRI][hapmap]
rs10789471	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1084086	0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs10890333	0.80[YRI][hapmap]
rs10890334	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs10890335	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs10890341	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs11211124	0.85[YRI][hapmap]
rs11211137	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11211139	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11211145	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11211146	0.94[YRI][hapmap]
rs11211147	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs11211149	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11211152	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs11211157	0.84[YRI][hapmap]
rs11211160	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11211161	0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap]
rs11211163	0.80[YRI][hapmap]
rs11211166	0.82[YRI][hapmap]
rs11211168	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11211169	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs11211171	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs11211173	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1135812	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs12023439	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12024590	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs12029322	0.85[YRI][hapmap]
rs12037459	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12043945	0.82[YRI][hapmap]
rs12049503	0.82[CHB][hapmap];0.80[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs12077621	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12091503	0.81[YRI][hapmap]
rs1547924	0.84[YRI][hapmap]
rs1547925	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs1972410	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs2050376	0.80[YRI][hapmap]
rs2152078	0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs2230658	0.80[YRI][hapmap]
rs2230659	0.82[YRI][hapmap]
rs2253862	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs2275085	0.80[YRI][hapmap]
rs2275086	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs28370457	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs28375469	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs28550303	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs28719889	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28890893	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2991979	0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap]
rs2991986	0.80[YRI][hapmap]
rs2991987	0.82[YRI][hapmap]
rs2991988	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs2991989	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap]
rs3014213	0.86[ASN][1000 genomes]
rs3014235	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs3014237	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs3014239	0.80[YRI][hapmap]
rs3014241	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs3014242	0.80[YRI][hapmap]
rs3014245	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs34768551	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3811436	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs4439382	0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs4559551	0.80[YRI][hapmap]
rs4564187	0.82[YRI][hapmap]
rs4607935	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs4609469	0.82[YRI][hapmap]
rs4633317	0.85[YRI][hapmap]
rs4660313	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4660863	0.85[YRI][hapmap]
rs4660880	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs499600	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]
rs512083	0.90[ASN][1000 genomes]
rs514595	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs518216	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs659437	0.85[EUR][1000 genomes]
rs6658700	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs666720	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6694889	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs6703748	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9429172	0.89[CHB][hapmap];1.00[JPT][hapmap]

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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3790585	Hs.396207	cis	multi-tissue	Pritchard
rs3790585	IPP	cis	multi-tissue	Pritchard
rs3790585	CCDC163P,LOC126661	cis	brain	BrainEAC
rs3790585	PRDX1	cis	Thyroid	GTEx
rs3790585	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs3790585	IPP	cis	Lymphoblastoid	GTEx
rs3790585		cis	Lymphoblastoid	GTEx
rs3790585	GPBP1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017000-46025800	Weak transcription	Spleen	Spleen
2	chr1:46017400-46027000	Weak transcription	Aorta	Aorta
3	chr1:46017400-46027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:46017800-46026800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:46017800-46026800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:46017800-46026800	Weak transcription	HSMMtube	muscle
7	chr1:46017800-46027200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:46017800-46027400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:46017800-46027400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:46017800-46027400	Weak transcription	Gastric	stomach
11	chr1:46017800-46032200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:46018000-46027400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:46018000-46032200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:46018400-46024800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:46018400-46025600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:46018400-46025800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:46018400-46026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:46018400-46026600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:46018400-46026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:46018400-46026800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:46018400-46027200	Weak transcription	Fetal Lung	lung
25	chr1:46018400-46027400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:46018400-46027400	Weak transcription	HUVEC	blood vessel
27	chr1:46018400-46029600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:46018400-46029800	Weak transcription	NHDF-Ad	bronchial
29	chr1:46018400-46032000	Weak transcription	Fetal Kidney	kidney
30	chr1:46018400-46032600	Weak transcription	Fetal Brain Male	brain
31	chr1:46018400-46036400	Strong transcription	Fetal Stomach	stomach
32	chr1:46018400-46036800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:46018400-46036800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:46018400-46036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:46018400-46037000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:46018600-46023600	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:46018600-46026800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:46018600-46026800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:46018600-46027000	Weak transcription	Esophagus	oesophagus
40	chr1:46018600-46032000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:46018600-46034200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:46018600-46036800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr1:46018600-46037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:46018600-46038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:46018800-46024400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:46019200-46032000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:46019800-46023400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:46020200-46026000	Weak transcription	Lung	lung
49	chr1:46020600-46025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:46020600-46032200	Weak transcription	Brain Angular Gyrus	brain

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