Variant report

Variant	rs12038046
Chromosome Location	chr1:93687526-93687527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93687387..93689162-chr1:93692159..93693688,2	K562	blood:
2	chr1:93681797..93684803-chr1:93687466..93690297,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1010476	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10874766	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164896	0.88[EUR][1000 genomes]
rs11164905	0.88[EUR][1000 genomes]
rs12027142	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12033147	0.88[EUR][1000 genomes]
rs12036057	0.80[EUR][1000 genomes]
rs12045001	0.88[EUR][1000 genomes]
rs12046063	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12563709	0.88[EUR][1000 genomes]
rs2255722	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2281524	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2484486	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783490	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2783493	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2783495	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783496	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783497	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783499	0.84[ASN][1000 genomes]
rs2783500	0.84[ASN][1000 genomes]
rs2783501	0.84[ASN][1000 genomes]
rs2783504	0.86[ASN][1000 genomes]
rs2783505	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815406	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2815415	0.87[ASN][1000 genomes]
rs2815429	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28782525	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2893242	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3087457	0.80[EUR][1000 genomes]
rs3904666	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs489183	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs556446	0.88[AMR][1000 genomes]
rs61799470	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61799496	0.86[ASN][1000 genomes]
rs61799497	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61799517	0.88[EUR][1000 genomes]
rs771454	0.80[EUR][1000 genomes]
rs771461	0.80[EUR][1000 genomes]
rs771465	0.80[EUR][1000 genomes]
rs771476	0.80[EUR][1000 genomes]
rs771479	0.80[EUR][1000 genomes]
rs771482	0.80[EUR][1000 genomes]
rs810027	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs12038046	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93647000-93756400	Weak transcription	Gastric	stomach
4	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
8	chr1:93654600-93708000	Weak transcription	Ovary	ovary
9	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
10	chr1:93660600-93705200	Weak transcription	Lung	lung
11	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:93661800-93702800	Weak transcription	Fetal Heart	heart
13	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
14	chr1:93663600-93705600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:93665400-93688800	Weak transcription	NHLF	lung
16	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
18	chr1:93665600-93697600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:93665600-93702600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:93665800-93693200	Weak transcription	Fetal Intestine Small	intestine
22	chr1:93665800-93706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:93667400-93687600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:93667400-93695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:93668800-93695200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:93668800-93697600	Weak transcription	Fetal Intestine Large	intestine
29	chr1:93668800-93708400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:93672200-93693200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:93672600-93708400	Weak transcription	Placenta	Placenta
32	chr1:93673800-93707400	Weak transcription	A549	lung
33	chr1:93674600-93692200	Weak transcription	Fetal Stomach	stomach
34	chr1:93675000-93693000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:93677200-93688800	Weak transcription	Fetal Kidney	kidney
36	chr1:93678000-93695200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:93682000-93704000	Weak transcription	Psoas Muscle	Psoas
38	chr1:93682400-93708800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:93682600-93691800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:93682800-93691200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:93683000-93687800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:93683000-93690400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:93683000-93691600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr1:93683000-93692000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:93683200-93689000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:93684000-93703200	Weak transcription	Hela-S3	cervix
47	chr1:93684600-93702600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:93684800-93688600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:93684800-93690000	Strong transcription	HMEC	breast
50	chr1:93684800-93708400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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