Variant report

Variant	rs509345
Chromosome Location	chr1:150276022-150276023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150273542..150277317-chr1:150288734..150292129,4	MCF-7	breast:
2	chr1:150240909..150242553-chr1:150274795..150276928,2	MCF-7	breast:
3	chr1:150272877..150274381-chr1:150274670..150277501,2	K562	blood:
4	chr1:150253424..150256570-chr1:150274213..150277391,3	MCF-7	breast:
5	chr1:150274604..150277468-chr1:150284678..150287144,3	K562	blood:
6	chr1:150274394..150277306-chr1:150282365..150283997,2	K562	blood:
7	chr1:150273843..150276533-chr1:150292946..150294730,3	MCF-7	breast:
8	chr1:150274556..150276296-chr1:150279435..150281772,2	K562	blood:
9	chr1:150274327..150277106-chr1:150277953..150280795,3	MCF-7	breast:
10	chr1:150273449..150279043-chr1:150279801..150282340,7	MCF-7	breast:
11	chr1:150269403..150271858-chr1:150275044..150277838,2	K562	blood:
12	chr1:150274446..150278949-chr1:150292354..150296326,6	MCF-7	breast:
13	chr1:150270315..150271818-chr1:150274900..150276885,2	MCF-7	breast:
14	chr1:150272468..150277468-chr1:150279289..150286428,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117360	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000117362	Chromatin interaction

Extended variants
information (count: 171 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:168)

rs_ID	r²[population]
rs10888578	0.85[GIH][hapmap]
rs1097067	0.85[ASN][1000 genomes]
rs1097068	0.85[ASN][1000 genomes]
rs1097070	0.85[ASN][1000 genomes]
rs1103115	0.88[ASN][1000 genomes]
rs11205357	0.93[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs11205359	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11205373	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11205382	0.81[CEU][hapmap]
rs1122967	0.94[ASN][1000 genomes]
rs1145583	0.88[ASN][1000 genomes]
rs11577600	0.84[ASN][1000 genomes]
rs11577843	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11581351	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11587575	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11587758	0.88[ASN][1000 genomes]
rs11590787	0.84[ASN][1000 genomes]
rs12028001	0.84[ASN][1000 genomes]
rs12040949	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12045304	0.84[ASN][1000 genomes]
rs1260367	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1260368	0.88[ASN][1000 genomes]
rs1260378	0.83[ASN][1000 genomes]
rs1260385	0.81[CEU][hapmap]
rs1260386	0.84[ASN][1000 genomes]
rs1260388	0.84[ASN][1000 genomes]
rs1260389	0.84[ASN][1000 genomes]
rs1260396	0.99[ASN][1000 genomes]
rs1260398	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1260400	0.87[ASN][1000 genomes]
rs1260404	0.89[ASN][1000 genomes]
rs1260405	0.89[ASN][1000 genomes]
rs1260406	0.89[ASN][1000 genomes]
rs1260407	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs1260409	0.87[ASN][1000 genomes]
rs1260411	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1260421	0.84[ASN][1000 genomes]
rs1260422	0.81[ASN][1000 genomes]
rs1260457	0.81[CEU][hapmap]
rs1260458	0.88[ASN][1000 genomes]
rs1260459	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12731296	0.80[CEU][hapmap]
rs12747669	0.83[ASN][1000 genomes]
rs1313568	0.81[CEU][hapmap]
rs1313570	0.88[ASN][1000 genomes]
rs1498308	0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs1614039	0.89[ASN][1000 genomes]
rs1617829	0.81[ASN][1000 genomes]
rs1625468	0.80[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs1627235	0.84[ASN][1000 genomes]
rs1631973	0.83[ASN][1000 genomes]
rs1694362	0.84[ASN][1000 genomes]
rs1694364	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1694369	0.88[ASN][1000 genomes]
rs1694370	0.94[ASN][1000 genomes]
rs1694375	0.96[ASN][1000 genomes]
rs1694377	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1694379	0.85[GIH][hapmap]
rs1694380	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1694381	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1694385	0.84[ASN][1000 genomes]
rs1694390	0.83[ASN][1000 genomes]
rs1747927	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17596326	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1776273	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1776274	0.97[ASN][1000 genomes]
rs1776276	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1932934	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2147324	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2264417	0.81[CEU][hapmap]
rs2264418	0.84[ASN][1000 genomes]
rs2274127	0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2454285	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2454286	0.85[ASN][1000 genomes]
rs2477121	0.87[ASN][1000 genomes]
rs2762860	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2794614	0.84[ASN][1000 genomes]
rs2794615	0.85[ASN][1000 genomes]
rs2794678	0.88[ASN][1000 genomes]
rs2794679	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2794681	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2794682	0.86[ASN][1000 genomes]
rs2794684	0.87[ASN][1000 genomes]
rs2794685	0.89[ASN][1000 genomes]
rs2797653	0.88[ASN][1000 genomes]
rs2873669	0.86[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs3125808	0.89[ASN][1000 genomes]
rs35057759	0.84[ASN][1000 genomes]
rs35915849	0.82[ASN][1000 genomes]
rs3896342	0.81[ASN][1000 genomes]
rs4333886	0.93[ASN][1000 genomes]
rs4446975	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap]
rs4451552	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4581308	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs471464	0.98[ASN][1000 genomes]
rs471738	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs486275	0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs488271	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4926394	0.85[ASN][1000 genomes]
rs4926395	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4926422	0.89[ASN][1000 genomes]
rs4926436	0.81[ASN][1000 genomes]
rs494041	0.82[ASN][1000 genomes]
rs494952	0.84[ASN][1000 genomes]
rs4970922	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs4970964	0.84[CEU][hapmap]
rs497128	0.88[ASN][1000 genomes]
rs500812	0.90[ASN][1000 genomes]
rs519126	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs521607	0.95[ASN][1000 genomes]
rs522435	0.90[ASN][1000 genomes]
rs543179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55742549	0.84[ASN][1000 genomes]
rs56214461	0.93[ASN][1000 genomes]
rs573351	0.83[ASN][1000 genomes]
rs578353	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs580060	0.99[ASN][1000 genomes]
rs580159	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6662108	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.81[ASN][1000 genomes]
rs6664703	0.84[CEU][hapmap]
rs6672808	0.81[ASN][1000 genomes]
rs6685252	0.95[ASN][1000 genomes]
rs6703652	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs696615	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs696616	0.80[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs696618	0.94[JPT][hapmap]
rs698913	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs698914	0.81[CEU][hapmap]
rs698916	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs698918	0.86[ASN][1000 genomes]
rs698919	0.84[ASN][1000 genomes]
rs698921	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs698923	0.83[ASN][1000 genomes]
rs7002	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs72696900	0.81[ASN][1000 genomes]
rs7411534	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7511649	0.86[CHB][hapmap]
rs7512552	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.94[ASN][1000 genomes]
rs7513182	0.80[CEU][hapmap]
rs7513205	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7517441	0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7523428	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7548085	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7554686	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8006	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs828783	0.83[ASN][1000 genomes]
rs832621	0.85[ASN][1000 genomes]
rs832622	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs834225	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs834228	0.81[ASN][1000 genomes]
rs834229	0.84[ASN][1000 genomes]
rs834230	0.84[ASN][1000 genomes]
rs834231	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs834232	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs834233	0.83[ASN][1000 genomes]
rs834234	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs834235	0.81[CEU][hapmap]
rs834236	0.84[ASN][1000 genomes]
rs834237	0.81[CEU][hapmap]
rs834238	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs834241	0.85[ASN][1000 genomes]
rs834242	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs834243	0.86[ASN][1000 genomes]
rs844309	0.84[ASN][1000 genomes]
rs9435997	0.93[ASN][1000 genomes]
rs9436009	0.84[CEU][hapmap]
rs9436108	0.83[ASN][1000 genomes]
rs9436112	0.94[JPT][hapmap];0.84[ASN][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	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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs509345	MRPS21	cis	cerebellum	SCAN
rs509345	MRPS21	cis	parietal	SCAN
rs509345	TARS2	cis	cerebellum	SCAN
rs509345	C1orf54	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150267000-150280000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:150267000-150280000	Weak transcription	Small Intestine	intestine
3	chr1:150267000-150284000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:150267000-150293200	Weak transcription	Stomach Mucosa	stomach
5	chr1:150267200-150280000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:150267200-150280000	Weak transcription	Esophagus	oesophagus
7	chr1:150267200-150286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:150267600-150276400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr1:150267600-150277800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:150267800-150276400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:150267800-150277000	Strong transcription	Adipose Nuclei	Adipose
12	chr1:150267800-150280800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:150267800-150281400	Strong transcription	Liver	Liver
14	chr1:150267800-150282000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:150268000-150281000	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:150268000-150281400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:150268000-150282600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:150268000-150293200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:150268200-150278800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:150268200-150279800	Weak transcription	Pancreas	Pancrea
21	chr1:150268200-150282600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:150268200-150282600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:150268200-150282800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:150268200-150282800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:150268200-150282800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:150268400-150276800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:150268600-150281000	Weak transcription	Fetal Brain Male	brain
28	chr1:150269000-150281400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:150269000-150282800	Strong transcription	Fetal Thymus	thymus
30	chr1:150269200-150277000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:150269200-150277600	Weak transcription	NHDF-Ad	bronchial
32	chr1:150269400-150282800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:150270200-150276400	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:150270200-150276400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:150270600-150277800	Strong transcription	Fetal Intestine Large	intestine
36	chr1:150271600-150284000	Weak transcription	Colonic Mucosa	Colon
37	chr1:150272200-150276400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:150272200-150276400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:150272200-150277000	Strong transcription	Osteobl	bone
40	chr1:150272200-150277200	Strong transcription	A549	lung
41	chr1:150272400-150276400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:150272400-150276400	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr1:150272600-150276200	Strong transcription	Placenta	Placenta
44	chr1:150272600-150276800	Strong transcription	HSMM	muscle
45	chr1:150272600-150282800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:150272800-150276800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:150273400-150278800	Strong transcription	Primary B cells from cord blood	blood
48	chr1:150273600-150277000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:150273600-150280800	Strong transcription	Thymus	Thymus
50	chr1:150273800-150276400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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