Variant report

Variant	rs500812
Chromosome Location	chr1:150269545-150269546
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150269191..150272405-chr1:150292812..150295253,3	MCF-7	breast:
2	chr1:150242514..150245022-chr1:150266520..150269823,3	K562	blood:
3	chr1:150269403..150271858-chr1:150275044..150277838,2	K562	blood:
4	chr1:150266649..150270690-chr1:150280933..150283523,3	K562	blood:
5	chr1:150266239..150267873-chr1:150268229..150269796,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187145	Chromatin interaction
ENSG00000117360	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1097067	0.91[EUR][1000 genomes]
rs1097068	0.91[EUR][1000 genomes]
rs1097070	0.92[EUR][1000 genomes]
rs1103115	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11205357	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11205359	0.89[ASN][1000 genomes]
rs1122967	0.90[ASN][1000 genomes]
rs1145583	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11577843	0.80[EUR][1000 genomes]
rs11587758	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11590787	0.80[EUR][1000 genomes]
rs12040949	0.80[AMR][1000 genomes]
rs12042229	0.80[AMR][1000 genomes]
rs12045304	0.80[EUR][1000 genomes]
rs1260367	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1260368	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1260378	0.82[EUR][1000 genomes]
rs1260386	0.83[EUR][1000 genomes]
rs1260388	0.83[EUR][1000 genomes]
rs1260389	0.83[EUR][1000 genomes]
rs1260394	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1260396	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1260398	0.89[ASN][1000 genomes]
rs1260400	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1260404	0.80[ASN][1000 genomes]
rs1260405	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1260406	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1260407	0.80[ASN][1000 genomes]
rs1260411	0.81[EUR][1000 genomes]
rs1260421	0.86[EUR][1000 genomes]
rs1260422	0.88[EUR][1000 genomes]
rs1260459	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1498308	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1614039	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1617829	0.83[EUR][1000 genomes]
rs1625468	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1627235	0.86[EUR][1000 genomes]
rs1694362	0.84[EUR][1000 genomes]
rs1694369	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1694370	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1694375	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1694377	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1694380	0.84[ASN][1000 genomes]
rs1694381	0.85[ASN][1000 genomes]
rs1694385	0.82[EUR][1000 genomes]
rs1747927	0.84[ASN][1000 genomes]
rs1776273	0.91[ASN][1000 genomes]
rs1776274	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1776276	0.82[ASN][1000 genomes]
rs1972031	0.80[AMR][1000 genomes]
rs2147324	0.88[ASN][1000 genomes]
rs2264418	0.83[EUR][1000 genomes]
rs2274127	0.88[ASN][1000 genomes]
rs2454285	0.83[ASN][1000 genomes]
rs2454286	0.89[EUR][1000 genomes]
rs2477121	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2762860	0.88[ASN][1000 genomes]
rs2794614	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2794615	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2794678	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2794679	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2794681	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2794682	0.90[EUR][1000 genomes]
rs2794684	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2794685	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2797653	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2873669	0.80[AMR][1000 genomes]
rs3125808	0.80[ASN][1000 genomes]
rs35057759	0.81[EUR][1000 genomes]
rs3896342	0.80[AMR][1000 genomes]
rs4333886	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4581308	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs471464	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs471738	0.89[ASN][1000 genomes]
rs486275	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs488271	0.84[ASN][1000 genomes]
rs4926422	0.80[ASN][1000 genomes]
rs4926437	0.80[AMR][1000 genomes]
rs494952	0.80[ASN][1000 genomes]
rs497128	0.84[ASN][1000 genomes]
rs509345	0.90[ASN][1000 genomes]
rs519126	0.83[ASN][1000 genomes]
rs521607	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs522435	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543179	0.91[ASN][1000 genomes]
rs55742549	0.80[EUR][1000 genomes]
rs56214461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs578353	0.84[ASN][1000 genomes]
rs580060	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580159	0.89[ASN][1000 genomes]
rs6672808	0.80[AMR][1000 genomes]
rs6685252	0.89[ASN][1000 genomes]
rs696616	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs698916	0.81[EUR][1000 genomes]
rs698919	0.81[EUR][1000 genomes]
rs698923	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7512552	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7517441	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7539458	0.80[AMR][1000 genomes]
rs7554686	0.89[ASN][1000 genomes]
rs8006	0.89[ASN][1000 genomes]
rs832622	0.80[EUR][1000 genomes]
rs834229	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs834230	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs834231	0.81[EUR][1000 genomes]
rs834232	0.89[EUR][1000 genomes]
rs834236	0.84[EUR][1000 genomes]
rs844309	0.83[EUR][1000 genomes]
rs9435997	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9436007	0.80[AMR][1000 genomes]
rs9436108	0.86[EUR][1000 genomes]
rs9436112	0.80[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs500812	MRPS21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150267000-150270400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:150267000-150271200	Weak transcription	Colonic Mucosa	Colon
3	chr1:150267000-150272200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:150267000-150272400	Weak transcription	Left Ventricle	heart
5	chr1:150267000-150272800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:150267000-150273800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150267000-150274000	Weak transcription	Aorta	Aorta
8	chr1:150267000-150274200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:150267000-150274400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:150267000-150274400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:150267000-150274600	Weak transcription	Gastric	stomach
12	chr1:150267000-150274600	Weak transcription	Ovary	ovary
13	chr1:150267000-150280000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:150267000-150280000	Weak transcription	Small Intestine	intestine
15	chr1:150267000-150284000	Weak transcription	Brain Substantia Nigra	brain
16	chr1:150267000-150293200	Weak transcription	Stomach Mucosa	stomach
17	chr1:150267200-150269600	Weak transcription	HSMMtube	muscle
18	chr1:150267200-150269800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:150267200-150269800	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:150267200-150269800	Weak transcription	Psoas Muscle	Psoas
21	chr1:150267200-150272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:150267200-150273000	Weak transcription	NH-A	brain
23	chr1:150267200-150273400	Weak transcription	Primary B cells from cord blood	blood
24	chr1:150267200-150273800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:150267200-150273800	Weak transcription	Right Ventricle	heart
26	chr1:150267200-150274400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:150267200-150274400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:150267200-150274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:150267200-150274400	Weak transcription	Fetal Kidney	kidney
30	chr1:150267200-150275600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:150267200-150276000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:150267200-150280000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:150267200-150280000	Weak transcription	Esophagus	oesophagus
34	chr1:150267200-150286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:150267400-150270200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:150267400-150270600	Weak transcription	Fetal Intestine Large	intestine
37	chr1:150267400-150272400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:150267400-150273600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:150267600-150269600	Strong transcription	Thymus	Thymus
40	chr1:150267600-150270800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:150267600-150273400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:150267600-150274400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:150267600-150274400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:150267600-150274400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:150267600-150275200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:150267600-150275400	Strong transcription	Fetal Stomach	stomach
47	chr1:150267600-150276400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:150267600-150277800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:150267800-150269600	Strong transcription	Osteobl	bone
50	chr1:150267800-150269800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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