Variant report

Variant	rs2783493
Chromosome Location	chr1:93635331-93635332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93634900..93638789-chr1:93645766..93648751,3	K562	blood:
2	chr1:93631186..93632972-chr1:93634578..93637260,2	K562	blood:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction
ENSG00000117500	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1010476	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10874766	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164896	0.82[EUR][1000 genomes]
rs11164905	0.82[EUR][1000 genomes]
rs12027142	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12033147	0.82[EUR][1000 genomes]
rs12038046	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044657	0.81[ASN][1000 genomes]
rs12045001	0.82[EUR][1000 genomes]
rs12046063	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12563709	0.82[EUR][1000 genomes]
rs2255722	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281524	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2484486	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2749732	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2783490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783495	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783496	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783497	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783499	0.83[ASN][1000 genomes]
rs2783500	0.83[ASN][1000 genomes]
rs2783501	0.83[ASN][1000 genomes]
rs2783504	0.82[ASN][1000 genomes]
rs2783505	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815415	0.83[ASN][1000 genomes]
rs2815429	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28782525	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2893242	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3904666	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs489183	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs556446	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs579138	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61799470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61799496	0.82[ASN][1000 genomes]
rs61799497	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61799517	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2783493	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:93582400-93642800	Weak transcription	Gastric	stomach
3	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
4	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
5	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
7	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
8	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
13	chr1:93620800-93635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:93621400-93635400	Weak transcription	Thymus	Thymus
15	chr1:93621400-93635600	Weak transcription	Lung	lung
16	chr1:93621400-93636800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:93621400-93637800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:93621400-93640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:93621400-93643000	Weak transcription	HMEC	breast
20	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
21	chr1:93621600-93641400	Weak transcription	NHEK	skin
22	chr1:93622200-93637200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:93622400-93636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:93624000-93637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:93624000-93643400	Weak transcription	NH-A	brain
26	chr1:93624000-93643600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:93624200-93636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:93624400-93643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:93624800-93636400	Weak transcription	Primary T cells from cord blood	blood
30	chr1:93624800-93641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:93624800-93643600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:93624800-93643600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:93625000-93636600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:93625000-93640000	Weak transcription	K562	blood
35	chr1:93625000-93641200	Weak transcription	HSMM	muscle
36	chr1:93625200-93635400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:93625200-93637200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:93625400-93636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:93625600-93637600	Weak transcription	NHLF	lung
40	chr1:93625800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:93625800-93635800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:93625800-93637000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:93625800-93637400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:93625800-93640200	Weak transcription	HUVEC	blood vessel
45	chr1:93625800-93641600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:93625800-93643400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:93626000-93641200	Weak transcription	NHDF-Ad	bronchial
48	chr1:93626200-93636000	Weak transcription	Fetal Thymus	thymus
49	chr1:93626200-93637000	Weak transcription	HepG2	liver
50	chr1:93627000-93637200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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