Variant report

Variant	rs6924482
Chromosome Location	chr6:34387216-34387217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34204321..34205956-chr6:34384818..34387597,2	K562	blood:
2	chr6:34385629..34388479-chr6:34571535..34574090,2	K562	blood:
3	chr6:34212124..34218246-chr6:34379945..34387655,19	K562	blood:
4	chr6:34162021..34165758-chr6:34380623..34387316,6	K562	blood:

Variant related genes	Relation type
ENSG00000137309	Chromatin interaction
ENSG00000186577	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs12664016	0.85[AFR][1000 genomes]
rs1811968	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006833	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206919	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs206920	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs206921	0.83[EUR][1000 genomes]
rs206924	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206936	0.86[EUR][1000 genomes]
rs206941	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs206942	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28847046	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3798556	0.83[EUR][1000 genomes]
rs3798560	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3913009	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3913010	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs410340	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs414739	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458576	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4587164	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs464553	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs568502	0.83[EUR][1000 genomes]
rs6457773	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6907486	0.83[EUR][1000 genomes]
rs6912971	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6924982	0.84[EUR][1000 genomes]
rs6925243	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6930978	0.84[EUR][1000 genomes]
rs7757586	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7757900	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7765498	0.83[EUR][1000 genomes]
rs7768978	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7773447	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7775635	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9366856	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368810	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9368813	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380433	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380435	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394214	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394218	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9461981	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9469775	0.85[EUR][1000 genomes]
rs9469778	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9469779	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9469780	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv981133	chr6:34385156-34393521	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6924482	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34372400-34389400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:34379200-34391800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:34381800-34391000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:34382000-34388000	Strong transcription	Dnd41	blood
5	chr6:34382000-34390000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:34382000-34391600	Strong transcription	NHEK	skin
7	chr6:34382000-34392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:34382000-34392000	Strong transcription	Primary T cells from cord blood	blood
9	chr6:34382400-34389400	Strong transcription	K562	blood
10	chr6:34382400-34389600	Weak transcription	Fetal Brain Male	brain
11	chr6:34382400-34391800	Strong transcription	NHDF-Ad	bronchial
12	chr6:34382400-34392000	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr6:34382400-34392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:34382400-34392000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:34382600-34387600	Weak transcription	Fetal Kidney	kidney
16	chr6:34382600-34387800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:34382600-34392000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:34383000-34391000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:34383000-34392200	Weak transcription	Right Atrium	heart
20	chr6:34383200-34389200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:34383200-34389400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:34383200-34391600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:34383200-34391600	Strong transcription	Fetal Thymus	thymus
24	chr6:34383400-34389400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:34383400-34390000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:34383400-34390000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:34383400-34390000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:34383400-34392000	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr6:34383400-34392000	Strong transcription	Fetal Lung	lung
30	chr6:34383400-34392600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:34383400-34392600	Strong transcription	Lung	lung
32	chr6:34383600-34389000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:34383600-34389400	Strong transcription	GM12878-XiMat	blood
34	chr6:34383600-34390200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:34383600-34391200	Strong transcription	Osteobl	bone
36	chr6:34383600-34391400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:34383600-34391400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:34383600-34391400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:34383600-34391600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:34383600-34391600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:34383600-34392000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:34383600-34392000	Strong transcription	Fetal Brain Female	brain
43	chr6:34383600-34392000	Strong transcription	Fetal Intestine Small	intestine
44	chr6:34383600-34392000	Strong transcription	Thymus	Thymus
45	chr6:34383600-34392200	Strong transcription	Fetal Muscle Leg	muscle
46	chr6:34383600-34392600	Strong transcription	Fetal Intestine Large	intestine
47	chr6:34383800-34387600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:34383800-34388000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:34383800-34388600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:34383800-34389400	Strong transcription	Primary T cells fromperipheralblood	blood

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