Variant report

Variant	rs3754214
Chromosome Location	chr1:150478623-150478624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:150478360-150478625	T-47D	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150458349..150461509-chr1:150477076..150480525,4	K562	blood:
2	chr1:150477376..150481637-chr1:150532635..150535451,4	K562	blood:
3	chr1:150476754..150479355-chr1:150479749..150481749,3	K562	blood:
4	chr1:150464206..150466889-chr1:150476033..150478905,2	MCF-7	breast:
5	chr1:150471391..150473524-chr1:150476982..150479373,2	K562	blood:
6	chr1:150458665..150461178-chr1:150476846..150479297,2	MCF-7	breast:
7	chr1:150477731..150480329-chr1:150524886..150527200,2	K562	blood:

No data

Variant related genes	Relation type
ECM1	TF binding region
ENSG00000143374	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143369	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10888583	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205370	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11205371	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11205373	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs11205375	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205382	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11205384	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11205387	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11581786	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12023277	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12031973	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1260385	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1260391	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1260407	0.95[CEU][hapmap]
rs1260419	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1260420	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1260424	0.85[AMR][1000 genomes]
rs1260457	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs1262432	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12731296	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12736375	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1313568	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1313569	0.81[ASN][1000 genomes]
rs13374465	0.80[ASN][1000 genomes]
rs1566225	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1694364	0.96[CEU][hapmap]
rs1694379	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1694380	0.96[CEU][hapmap]
rs1694386	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1776270	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1815545	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1932934	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2012751	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2133129	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2264417	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2275246	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35705743	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35784258	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3754217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850844	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4446975	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4451552	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs488271	0.96[CEU][hapmap]
rs4926395	0.82[EUR][1000 genomes]
rs4926435	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4970922	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970963	0.89[ASN][1000 genomes]
rs4970964	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970971	0.87[EUR][1000 genomes]
rs4970979	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971010	0.91[CEU][hapmap]
rs5011187	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs578353	0.95[CEU][hapmap]
rs6664703	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678973	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6684939	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687311	0.88[AMR][1000 genomes]
rs6699093	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs696615	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs696617	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs698913	0.96[CEU][hapmap]
rs698914	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs698920	0.85[AMR][1000 genomes]
rs698921	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs698922	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7366347	0.81[AMR][1000 genomes]
rs7411534	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7513182	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7513247	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548085	0.96[CEU][hapmap]
rs7553647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006	0.96[CEU][hapmap]
rs832621	0.82[EUR][1000 genomes]
rs834225	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs834234	0.95[CEU][hapmap]
rs834235	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs834237	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs834238	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs834242	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs863862	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs875514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9436009	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9436010	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9436116	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9436118	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9436120	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9436122	0.87[ASN][1000 genomes]
rs9661040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	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
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3754214	MRPS21	cis	Thyroid	GTEx
rs3754214	MRPS21	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150460600-150480200	Weak transcription	Right Atrium	heart
2	chr1:150460600-150480200	Weak transcription	Stomach Mucosa	stomach
3	chr1:150460800-150480000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:150461000-150486800	Weak transcription	Fetal Heart	heart
5	chr1:150461400-150480000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:150461400-150480400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:150461400-150480400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:150461400-150480600	Strong transcription	Fetal Intestine Large	intestine
9	chr1:150462000-150480000	Strong transcription	Fetal Stomach	stomach
10	chr1:150462000-150480600	Strong transcription	Fetal Intestine Small	intestine
11	chr1:150462000-150485800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:150463200-150479800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:150464800-150480200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:150468000-150479800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:150468000-150480800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:150468200-150480200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:150468400-150479600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:150468400-150479800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:150468400-150479800	Strong transcription	Fetal Thymus	thymus
20	chr1:150468400-150480200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:150468400-150480200	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:150468400-150480800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:150468600-150479600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:150468600-150479800	Strong transcription	Adipose Nuclei	Adipose
25	chr1:150468600-150480200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:150468600-150481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:150468600-150481000	Strong transcription	Thymus	Thymus
28	chr1:150468800-150479800	Strong transcription	Lung	lung
29	chr1:150468800-150480000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:150468800-150483800	Strong transcription	Brain Germinal Matrix	brain
31	chr1:150471600-150480800	Strong transcription	Liver	Liver
32	chr1:150471800-150487400	Weak transcription	Fetal Brain Male	brain
33	chr1:150472400-150480000	Weak transcription	NHDF-Ad	bronchial
34	chr1:150473800-150480000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:150474400-150482000	Strong transcription	Primary T cells from cord blood	blood
36	chr1:150474600-150480200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:150474800-150479200	Strong transcription	Colonic Mucosa	Colon
38	chr1:150474800-150479600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:150474800-150479800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr1:150474800-150480200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:150474800-150480400	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:150475000-150479000	Strong transcription	Fetal Lung	lung
43	chr1:150475000-150479600	Strong transcription	Brain Substantia Nigra	brain
44	chr1:150475000-150479600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:150475000-150479600	Strong transcription	NHLF	lung
46	chr1:150475000-150479800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:150475000-150480200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:150475000-150480600	Strong transcription	Dnd41	blood
49	chr1:150475000-150485400	Strong transcription	Fetal Brain Female	brain
50	chr1:150475200-150479600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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