Variant report

Variant	rs4814243
Chromosome Location	chr20:1409435-1409436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1408022..1413976-chr20:1445856..1450713,7	K562	blood:
2	chr20:1408581..1410916-chr20:1448637..1451105,2	K562	blood:
3	chr20:1408801..1411564-chr20:1423013..1426503,3	K562	blood:
4	chr20:1406951..1409518-chr20:1413752..1415775,2	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11087052	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs13063	0.84[JPT][hapmap]
rs1884388	0.82[ASN][1000 genomes]
rs1884389	0.82[CHD][hapmap]
rs1884391	0.84[JPT][hapmap]
rs1998007	0.85[ASN][1000 genomes]
rs2144542	0.88[ASN][1000 genomes]
rs2144543	0.88[ASN][1000 genomes]
rs2207828	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207829	0.85[ASN][1000 genomes]
rs2207830	0.91[ASN][1000 genomes]
rs3171292	0.84[JPT][hapmap]
rs3210915	0.84[JPT][hapmap]
rs36018423	0.88[ASN][1000 genomes]
rs3829698	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs4352285	0.84[JPT][hapmap]
rs4546067	0.84[JPT][hapmap]
rs4813133	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4814229	0.80[ASN][1000 genomes]
rs4814231	0.85[ASN][1000 genomes]
rs4814237	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs4814240	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs4814244	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs5019244	0.88[ASN][1000 genomes]
rs6033691	0.85[ASN][1000 genomes]
rs6033697	0.80[ASN][1000 genomes]
rs6033698	0.80[ASN][1000 genomes]
rs6033707	0.85[ASN][1000 genomes]
rs6033709	0.80[ASN][1000 genomes]
rs6033710	0.80[ASN][1000 genomes]
rs6033715	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs6033726	0.88[ASN][1000 genomes]
rs6033728	0.88[ASN][1000 genomes]
rs6033729	0.88[ASN][1000 genomes]
rs6033732	0.88[ASN][1000 genomes]
rs6033744	0.88[ASN][1000 genomes]
rs6033753	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042066	0.80[ASN][1000 genomes]
rs6042071	0.80[ASN][1000 genomes]
rs6042072	0.85[ASN][1000 genomes]
rs6042074	0.85[ASN][1000 genomes]
rs6042088	0.80[ASN][1000 genomes]
rs6042091	0.85[ASN][1000 genomes]
rs6042117	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs6042118	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs6042131	0.88[ASN][1000 genomes]
rs6042160	0.88[ASN][1000 genomes]
rs6042170	0.88[ASN][1000 genomes]
rs6042172	0.88[ASN][1000 genomes]
rs6042175	0.88[ASN][1000 genomes]
rs6042197	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042207	0.88[ASN][1000 genomes]
rs6042208	0.88[ASN][1000 genomes]
rs6042209	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6042244	0.84[JPT][hapmap]
rs6042292	0.84[JPT][hapmap]
rs6042354	0.84[JPT][hapmap]
rs6074593	0.85[ASN][1000 genomes]
rs6074623	0.95[ASN][1000 genomes]
rs6079009	0.85[ASN][1000 genomes]
rs6079010	0.85[ASN][1000 genomes]
rs6079012	0.85[ASN][1000 genomes]
rs6079013	0.85[ASN][1000 genomes]
rs6079015	0.85[ASN][1000 genomes]
rs6105079	0.85[ASN][1000 genomes]
rs6105081	0.85[ASN][1000 genomes]
rs6105102	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs6105110	0.85[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6109825	0.85[ASN][1000 genomes]
rs6109893	0.88[ASN][1000 genomes]
rs6109894	0.88[ASN][1000 genomes]
rs6109912	0.88[ASN][1000 genomes]
rs6131468	0.80[ASN][1000 genomes]
rs6134916	0.88[ASN][1000 genomes]
rs6514382	0.85[ASN][1000 genomes]
rs6514383	0.85[ASN][1000 genomes]
rs750424	0.88[ASN][1000 genomes]
rs8124053	0.80[ASN][1000 genomes]
rs873523	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910620	0.84[JPT][hapmap]
rs926977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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
rs4814243	SIRPB1	cis	parietal	SCAN
rs4814243	NSFL1C	cis	cerebellum	SCAN
rs4814243	SNORA51	cis	cerebellum	SCAN
rs4814243	FKBP1A	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

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	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
4	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
5	chr20:1405000-1409600	Weak transcription	Stomach Mucosa	stomach
6	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
7	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
11	chr20:1405600-1409800	Weak transcription	HMEC	breast
12	chr20:1406000-1410000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:1407800-1410800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
15	chr20:1408400-1411000	Enhancers	K562	blood
16	chr20:1408600-1409800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:1408600-1414400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
19	chr20:1408800-1409800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr20:1408800-1409800	Weak transcription	NHEK	skin
21	chr20:1408800-1410000	Weak transcription	Fetal Intestine Large	intestine
22	chr20:1408800-1410400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:1408800-1410400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:1408800-1410600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr20:1408800-1410600	Weak transcription	Adipose Nuclei	Adipose
26	chr20:1408800-1410600	Weak transcription	NHDF-Ad	bronchial
27	chr20:1408800-1410800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr20:1408800-1414200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:1408800-1414400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr20:1408800-1415000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:1409000-1410600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:1409000-1410800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:1409000-1410800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr20:1409000-1410800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr20:1409000-1410800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:1409000-1411200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr20:1409000-1411200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr20:1409000-1411400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
47	chr20:1409200-1409600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr20:1409200-1409600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:1409200-1409800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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