Variant report

Variant	rs3020004
Chromosome Location	chr11:93918837-93918838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93917086..93919356-chr11:93920990..93923600,2	K562	blood:

Variant related genes	Relation type
ENSG00000256745	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1014499	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10458852	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10765657	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10765658	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10765660	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10831169	0.94[EUR][1000 genomes]
rs10831173	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10831174	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10831175	0.81[AMR][1000 genomes]
rs10831176	0.91[EUR][1000 genomes]
rs10831184	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11020678	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11020679	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11020703	0.88[EUR][1000 genomes]
rs11020719	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12362988	0.81[AMR][1000 genomes]
rs12366039	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12792677	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12803129	0.82[EUR][1000 genomes]
rs12808853	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1361929	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1541301	0.94[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16920039	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs1789652	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792632	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1833063	0.83[AMR][1000 genomes]
rs1857680	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1944436	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2000956	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2156627	0.91[EUR][1000 genomes]
rs3020016	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4597032	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4753131	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4753132	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4753548	0.81[AMR][1000 genomes]
rs4753569	0.86[AMR][1000 genomes]
rs480710	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs581771	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs613234	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6483324	0.81[EUR][1000 genomes]
rs655358	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689315	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7115129	0.80[EUR][1000 genomes]
rs7118270	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7130456	0.82[EUR][1000 genomes]
rs7927338	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7927496	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7936241	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7944234	0.82[EUR][1000 genomes]
rs871244	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898184	chr11:93741612-93969726	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv1046092	chr11:93833446-93964452	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
3	nsv898185	chr11:93851048-93927529	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv469980	chr11:93864321-93962121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv468795	chr11:93864321-93964917	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv555966	chr11:93864321-93964917	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1038294	chr11:93918837-93982605	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3020004	GPR83	cis	parietal	SCAN
rs3020004	RP11-680H20.2	cis	Artery Tibial	GTEx
rs3020004	PANX1	cis	parietal	SCAN
rs3020004	MRE11A	cis	parietal	SCAN
rs3020004	PANX1	cis	lymphoblastoid	seeQTL
rs3020004	GPR83	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93897800-93920000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:93901400-93921200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:93904800-93920000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:93905400-93919600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:93907200-93919600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:93910400-93919000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:93910600-93919200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:93912200-93921000	Weak transcription	Brain Anterior Caudate	brain
9	chr11:93913600-93919200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:93913600-93929400	Weak transcription	Gastric	stomach
11	chr11:93913800-93921400	Weak transcription	Fetal Brain Male	brain
12	chr11:93914400-93920400	Weak transcription	Primary B cells from cord blood	blood
13	chr11:93914800-93919800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:93914800-93920400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:93914800-93920600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:93914800-93921000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:93914800-93921600	Weak transcription	Thymus	Thymus
18	chr11:93914800-93926200	Weak transcription	Esophagus	oesophagus
19	chr11:93914800-93926200	Weak transcription	Spleen	Spleen
20	chr11:93915000-93921000	Weak transcription	Right Ventricle	heart
21	chr11:93915400-93919000	Weak transcription	Fetal Brain Female	brain
22	chr11:93915600-93920400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:93915600-93929400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:93915800-93919000	Enhancers	Fetal Kidney	kidney
25	chr11:93916200-93920800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:93916200-93921200	Weak transcription	Primary T cells from cord blood	blood
27	chr11:93916400-93922000	Weak transcription	Brain Germinal Matrix	brain
28	chr11:93916800-93920200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:93916800-93920200	Enhancers	NHLF	lung
30	chr11:93916800-93920600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:93916800-93926200	Weak transcription	HMEC	breast
32	chr11:93917000-93919400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:93917000-93919400	Enhancers	HSMMtube	muscle
34	chr11:93917000-93919600	Enhancers	HSMM	muscle
35	chr11:93917000-93920800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:93917200-93919800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:93917200-93919800	Weak transcription	A549	lung
38	chr11:93917200-93920200	Weak transcription	Dnd41	blood
39	chr11:93917200-93926200	Weak transcription	NHEK	skin
40	chr11:93917400-93919000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:93917400-93919000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr11:93917400-93919200	Enhancers	Fetal Lung	lung
43	chr11:93917400-93919400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr11:93917400-93919400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:93917400-93919400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr11:93917400-93920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:93917400-93921000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:93917400-93921200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:93917400-93922000	Weak transcription	Lung	lung
50	chr11:93917600-93919200	Weak transcription	Fetal Intestine Large	intestine

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