Variant report

Variant	rs12747669
Chromosome Location	chr1:150268622-150268623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150204882..150207260-chr1:150266148..150269015,2	MCF-7	breast:
2	chr1:150242514..150245022-chr1:150266520..150269823,3	K562	blood:
3	chr1:150264496..150269056-chr1:150292330..150296241,7	MCF-7	breast:
4	chr1:150266649..150270690-chr1:150280933..150283523,3	K562	blood:
5	chr1:150266239..150267873-chr1:150268229..150269796,2	MCF-7	breast:
6	chr1:150206170..150208675-chr1:150264452..150269195,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187145	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10888578	0.85[EUR][1000 genomes]
rs10888579	0.86[EUR][1000 genomes]
rs1097066	0.82[EUR][1000 genomes]
rs1097069	0.81[EUR][1000 genomes]
rs11205357	0.84[ASN][1000 genomes]
rs11205359	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1122967	0.83[ASN][1000 genomes]
rs11811885	0.90[EUR][1000 genomes]
rs12093148	0.89[EUR][1000 genomes]
rs1260385	0.84[EUR][1000 genomes]
rs1260396	0.83[ASN][1000 genomes]
rs1260398	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1260401	0.82[EUR][1000 genomes]
rs1260403	0.84[EUR][1000 genomes]
rs1260404	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1260407	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1260408	0.84[EUR][1000 genomes]
rs1260409	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12739706	0.85[EUR][1000 genomes]
rs1313570	0.80[EUR][1000 genomes]
rs1614039	0.86[ASN][1000 genomes]
rs1694364	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1694370	0.82[ASN][1000 genomes]
rs1694375	0.85[ASN][1000 genomes]
rs1694379	0.86[EUR][1000 genomes]
rs1694380	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1694381	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1747927	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1776272	0.84[EUR][1000 genomes]
rs1776273	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1776274	0.84[ASN][1000 genomes]
rs1776275	0.90[EUR][1000 genomes]
rs1776276	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2147324	0.81[ASN][1000 genomes]
rs2274127	0.81[ASN][1000 genomes]
rs2454285	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2477121	0.80[ASN][1000 genomes]
rs2762860	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3125808	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35915849	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818978	0.88[EUR][1000 genomes]
rs4581308	0.83[ASN][1000 genomes]
rs471464	0.82[ASN][1000 genomes]
rs471738	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs488271	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4926422	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs494041	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs494952	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs497128	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509345	0.83[ASN][1000 genomes]
rs519126	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs543179	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs573351	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs578353	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs580060	0.83[ASN][1000 genomes]
rs580159	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6685252	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6693697	0.82[EUR][1000 genomes]
rs696615	0.80[EUR][1000 genomes]
rs698914	0.85[EUR][1000 genomes]
rs698917	0.83[EUR][1000 genomes]
rs7512552	0.83[ASN][1000 genomes]
rs7544900	0.87[EUR][1000 genomes]
rs7554686	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8006	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs834225	0.85[EUR][1000 genomes]
rs834243	0.80[EUR][1000 genomes]
rs9126	0.85[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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12747669	MRPS21	cis	Heart Left Ventricle	GTEx
rs12747669	MRPS21	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150267000-150269200	Weak transcription	Right Atrium	heart
2	chr1:150267000-150270400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:150267000-150271200	Weak transcription	Colonic Mucosa	Colon
4	chr1:150267000-150272200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:150267000-150272400	Weak transcription	Left Ventricle	heart
6	chr1:150267000-150272800	Weak transcription	Primary T cells from cord blood	blood
7	chr1:150267000-150273800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:150267000-150274000	Weak transcription	Aorta	Aorta
9	chr1:150267000-150274200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:150267000-150274400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:150267000-150274400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:150267000-150274600	Weak transcription	Gastric	stomach
13	chr1:150267000-150274600	Weak transcription	Ovary	ovary
14	chr1:150267000-150280000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:150267000-150280000	Weak transcription	Small Intestine	intestine
16	chr1:150267000-150284000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:150267000-150293200	Weak transcription	Stomach Mucosa	stomach
18	chr1:150267200-150268800	Weak transcription	Lung	lung
19	chr1:150267200-150269000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:150267200-150269600	Weak transcription	HSMMtube	muscle
21	chr1:150267200-150269800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:150267200-150269800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:150267200-150269800	Weak transcription	Psoas Muscle	Psoas
24	chr1:150267200-150272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:150267200-150273000	Weak transcription	NH-A	brain
26	chr1:150267200-150273400	Weak transcription	Primary B cells from cord blood	blood
27	chr1:150267200-150273800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:150267200-150273800	Weak transcription	Right Ventricle	heart
29	chr1:150267200-150274400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:150267200-150274400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:150267200-150274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:150267200-150274400	Weak transcription	Fetal Kidney	kidney
33	chr1:150267200-150275600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:150267200-150276000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:150267200-150280000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:150267200-150280000	Weak transcription	Esophagus	oesophagus
37	chr1:150267200-150286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:150267400-150268800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:150267400-150269000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:150267400-150269000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:150267400-150269000	Genic enhancers	Fetal Thymus	thymus
42	chr1:150267400-150269400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:150267400-150270200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:150267400-150270600	Weak transcription	Fetal Intestine Large	intestine
45	chr1:150267400-150272400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:150267400-150273600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:150267600-150269400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:150267600-150269600	Strong transcription	Thymus	Thymus
49	chr1:150267600-150270800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:150267600-150273400	Strong transcription	H1 Cell Line	embryonic stem cell

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