Variant report

Variant	rs12028305
Chromosome Location	chr1:225708026-225708027
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	chr1:225704786..225708350-chr1:225708492..225710197,3	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10753406	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799311	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799313	0.82[ASN][1000 genomes]
rs10799314	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799316	0.84[ASN][1000 genomes]
rs10799317	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10799318	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10799319	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10915830	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10915833	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915834	0.94[EUR][1000 genomes]
rs10915835	0.82[ASN][1000 genomes]
rs10915837	0.84[ASN][1000 genomes]
rs10915839	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10915847	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584675	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1222440	0.82[ASN][1000 genomes]
rs12729655	0.84[ASN][1000 genomes]
rs2639703	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2639716	0.82[EUR][1000 genomes]
rs2657564	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2657569	0.82[EUR][1000 genomes]
rs2840958	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2840967	0.82[EUR][1000 genomes]
rs2840968	0.82[EUR][1000 genomes]
rs3820226	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856156	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4653643	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476540	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487591	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498350	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510293	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511649	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516249	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551996	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554744	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554992	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561656	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576861	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426076	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426078	0.82[ASN][1000 genomes]
rs6668770	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6676201	0.84[ASN][1000 genomes]
rs6678806	0.83[ASN][1000 genomes]
rs6702555	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6751	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712062	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7515907	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515963	0.84[ASN][1000 genomes]
rs7524766	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540181	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541598	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7555139	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555553	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs812523	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs947034	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9804142	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12028305	RP11-496N12.9	cis	Thyroid	GTEx
rs12028305	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225688800-225711400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
4	chr1:225697200-225711200	Weak transcription	Fetal Heart	heart
5	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
6	chr1:225697400-225715400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:225697800-225708600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
10	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:225700000-225726400	Weak transcription	HMEC	breast
12	chr1:225700400-225708400	Weak transcription	Dnd41	blood
13	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
15	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
16	chr1:225701800-225710800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:225704200-225721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:225704400-225711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:225705600-225708600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225705600-225710200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:225705600-225711000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:225705600-225714000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:225705600-225714600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:225705600-225715800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:225705600-225717600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:225705800-225708600	Weak transcription	Spleen	Spleen
28	chr1:225705800-225710400	Weak transcription	Fetal Brain Male	brain
29	chr1:225705800-225710600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:225705800-225710800	Weak transcription	HSMMtube	muscle
31	chr1:225705800-225711000	Weak transcription	Fetal Brain Female	brain
32	chr1:225705800-225713200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:225705800-225714000	Weak transcription	Left Ventricle	heart
34	chr1:225705800-225714200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:225705800-225714600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:225705800-225716000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:225705800-225716800	Weak transcription	HepG2	liver
38	chr1:225705800-225717000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:225705800-225717400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:225705800-225717400	Weak transcription	Esophagus	oesophagus
41	chr1:225705800-225718800	Weak transcription	Lung	lung
42	chr1:225705800-225726600	Weak transcription	NHEK	skin
43	chr1:225706800-225710800	Weak transcription	Stomach Mucosa	stomach
44	chr1:225707000-225717400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:225707200-225708200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:225707200-225710200	Weak transcription	Fetal Intestine Large	intestine
47	chr1:225707200-225711200	Weak transcription	Right Ventricle	heart
48	chr1:225707200-225714200	Weak transcription	Ovary	ovary
49	chr1:225707200-225715400	Weak transcription	Pancreas	Pancrea
50	chr1:225707200-225716600	Weak transcription	Fetal Stomach	stomach

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