Variant report

Variant	rs2203039
Chromosome Location	chr4:120132347-120132348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:120132301-120134737	U87	brain:	n/a	n/a
2	POLR2A	chr4:120132113-120135034	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:120131791-120132931	K562	blood:	n/a	n/a
4	POLR2A	chr4:120132342-120134815	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr4:120131824-120132524	HUVEC	blood vessel:	n/a	chr4:120132083-120132094 chr4:120132085-120132094 chr4:120132159-120132168 chr4:120132085-120132093 chr4:120132086-120132093 chr4:120132084-120132093
6	POLR2A	chr4:120132327-120134731	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:120107053..120109251-chr4:120131734..120133629,2	MCF-7	breast:
2	chr4:120059391..120062207-chr4:120131058..120133617,2	MCF-7	breast:
3	chr4:120132319..120136069-chr4:120219720..120222326,6	MCF-7	breast:
4	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
5	chr4:120130951..120136158-chr4:120218006..120223072,8	K562	blood:
6	chr4:120131661..120133788-chr4:120986266..120989312,3	K562	blood:
7	chr4:119903589..119905538-chr4:120130770..120132703,2	MCF-7	breast:

Variant related genes	Relation type
USP53	TF binding region
ENSG00000164109	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10003567	0.90[CEU][hapmap]
rs10006259	0.90[CEU][hapmap]
rs10006304	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10010696	0.81[EUR][1000 genomes]
rs10013032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013042	0.90[CEU][hapmap]
rs10022508	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031033	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1011054	0.81[CEU][hapmap]
rs1033087	0.89[ASN][1000 genomes]
rs10518300	0.90[CEU][hapmap]
rs11098490	0.85[ASN][1000 genomes]
rs11098491	0.85[ASN][1000 genomes]
rs11098492	0.87[ASN][1000 genomes]
rs11098493	0.88[ASN][1000 genomes]
rs11098499	0.81[CEU][hapmap]
rs11098501	0.90[CEU][hapmap]
rs11726229	0.80[CEU][hapmap]
rs11732686	0.89[CEU][hapmap]
rs11733239	0.84[ASN][1000 genomes]
rs11944880	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs12186259	0.81[EUR][1000 genomes]
rs12502503	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12507565	0.90[CEU][hapmap]
rs12509054	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12511640	0.90[CEU][hapmap]
rs12513083	0.89[CEU][hapmap]
rs12513191	0.87[ASN][1000 genomes]
rs12711071	0.90[CEU][hapmap]
rs13113112	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs13114751	0.81[EUR][1000 genomes]
rs13120560	0.85[ASN][1000 genomes]
rs13123591	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13126596	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129661	0.80[CEU][hapmap]
rs13136593	0.87[ASN][1000 genomes]
rs13138782	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1397608	0.81[EUR][1000 genomes]
rs1511017	0.90[CEU][hapmap]
rs1511018	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1511019	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1511025	0.90[CEU][hapmap];0.88[MEX][hapmap]
rs1546503	0.90[CEU][hapmap]
rs17839089	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980025	0.90[CEU][hapmap]
rs1980026	0.90[CEU][hapmap]
rs2036861	0.89[ASN][1000 genomes]
rs28452522	0.94[ASN][1000 genomes]
rs35271032	0.81[EUR][1000 genomes]
rs35916640	0.80[EUR][1000 genomes]
rs3749591	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs4145951	0.80[EUR][1000 genomes]
rs4355373	0.85[ASN][1000 genomes]
rs4833612	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833613	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs56122576	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56386062	0.81[EUR][1000 genomes]
rs6534130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68128210	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815725	0.81[EUR][1000 genomes]
rs6822498	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6826823	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6832670	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837898	0.81[CEU][hapmap]
rs6838674	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845702	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6849889	0.81[CEU][hapmap]
rs6851130	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851169	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs714899	0.86[CEU][hapmap]
rs7441137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659194	0.81[CEU][hapmap]
rs7661020	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7672594	0.90[CEU][hapmap]
rs7685268	0.81[EUR][1000 genomes]
rs878372	0.90[CEU][hapmap]
rs907205	0.90[CEU][hapmap]
rs951570	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991959	0.90[CEU][hapmap]
rs9993110	0.86[ASN][1000 genomes]
rs9995277	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9996382	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9999724	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2203039	RP11-384K6.6	cis	Whole Blood	GTEx
rs2203039	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs2203039	USP53	cis	parietal	SCAN
rs2203039	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2203039	BBS7	cis	cerebellum	SCAN
rs2203039	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	lesional skin	skin_eQTL
rs2203039	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs2203039	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs2203039	USP53	cis	cerebellum	SCAN
rs2203039	RP11-384K6.6	cis	Artery Tibial	GTEx
rs2203039	C4orf3	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120117600-120133200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120126400-120132400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:120126400-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:120126400-120132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:120126400-120132400	Enhancers	HUVEC	blood vessel
7	chr4:120126400-120132600	Weak transcription	Right Atrium	heart
8	chr4:120127400-120132400	Enhancers	NHLF	lung
9	chr4:120128000-120132800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:120128400-120132400	Weak transcription	Adipose Nuclei	Adipose
11	chr4:120128600-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:120128600-120132400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:120128600-120132600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:120129000-120132800	Weak transcription	Fetal Heart	heart
15	chr4:120129200-120132400	Weak transcription	Fetal Lung	lung
16	chr4:120129600-120132800	Enhancers	Hela-S3	cervix
17	chr4:120129800-120132400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:120130000-120132600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:120130400-120132400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:120130600-120132800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:120130800-120132600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:120130800-120132800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:120131000-120132400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr4:120131000-120132800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:120131200-120132400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:120131200-120132400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:120131200-120132400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:120131200-120132400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:120131200-120132400	Weak transcription	NH-A	brain
30	chr4:120131200-120132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:120131200-120132800	Weak transcription	Stomach Mucosa	stomach
32	chr4:120131200-120133000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:120131400-120132800	Weak transcription	HSMMtube	muscle
34	chr4:120131600-120132600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:120131600-120132600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:120131800-120132400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr4:120131800-120132600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:120131800-120132600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:120131800-120132600	Flanking Active TSS	NHEK	skin
40	chr4:120132000-120132400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr4:120132000-120137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:120132200-120132400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:120132200-120132400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr4:120132200-120132400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
45	chr4:120132200-120132400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr4:120132200-120132400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:120132200-120132400	Enhancers	Liver	Liver
48	chr4:120132200-120132400	Enhancers	HSMM	muscle
49	chr4:120132200-120132600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:120132200-120132600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell

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