Variant report

Variant	rs6074625
Chromosome Location	chr20:1408490-1408491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1403838..1406635-chr20:1407133..1408659,2	K562	blood:
2	chr20:1408022..1413976-chr20:1445856..1450713,7	K562	blood:
3	chr20:1406951..1409518-chr20:1413752..1415775,2	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2207831	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074603	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074608	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6074609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079018	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079040	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079044	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079045	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079053	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079055	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6079082	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62186872	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62186873	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7270038	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7271175	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7353854	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6074625	SOX12	cis	cerebellum	SCAN
rs6074625	SIRPG	cis	lymphoblastoid	seeQTL
rs6074625	NSFL1C	cis	cerebellum	SCAN
rs6074625	SIRPB2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1400000-1410600	Weak transcription	Osteobl	bone
3	chr20:1404000-1409000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
5	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
6	chr20:1405000-1409600	Weak transcription	Stomach Mucosa	stomach
7	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
8	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
12	chr20:1405600-1409800	Weak transcription	HMEC	breast
13	chr20:1406000-1410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:1406600-1409000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr20:1406600-1409000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr20:1406800-1408600	Enhancers	Primary hematopoietic stem cells	blood
17	chr20:1406800-1408800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr20:1406800-1409000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr20:1406800-1409000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:1407000-1408800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr20:1407000-1408800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:1407000-1408800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr20:1407000-1409000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr20:1407200-1408800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr20:1407200-1409000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:1407200-1409000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:1407200-1409000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr20:1407400-1408800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr20:1407600-1409200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr20:1407800-1408800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:1407800-1408800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr20:1407800-1408800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:1407800-1408800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr20:1407800-1409200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr20:1407800-1410800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr20:1408000-1408800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr20:1408000-1408800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:1408000-1408800	Enhancers	Fetal Thymus	thymus
39	chr20:1408000-1409200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr20:1408200-1408600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr20:1408200-1408600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr20:1408200-1408600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:1408200-1408800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:1408200-1408800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr20:1408200-1408800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr20:1408200-1408800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr20:1408200-1408800	Enhancers	Adipose Nuclei	Adipose
48	chr20:1408200-1408800	Enhancers	Fetal Intestine Large	intestine
49	chr20:1408200-1408800	Enhancers	Fetal Muscle Trunk	muscle
50	chr20:1408200-1408800	Enhancers	Lung	lung

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