Variant report

Variant	rs539602
Chromosome Location	chr1:155899020-155899021
allele	A/T
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	FOS	chr1:155898856-155899406	MCF10A-Er-Src	breast:	n/a	chr1:155899039-155899046 chr1:155899036-155899047 chr1:155898883-155898895
2	MYC	chr1:155898834-155899226	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:155899013-155899147	K562	blood:	n/a	n/a
4	POLR2A	chr1:155898928-155899204	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:155898974-155899062	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:155898871-155899219	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:155898872-155899249	GM12892	blood:	n/a	n/a
8	MYC	chr1:155898886-155899208	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:155898860-155899210	GM12878	blood:	n/a	n/a
10	FOS	chr1:155898858-155899221	MCF10A-Er-Src	breast:	n/a	chr1:155899039-155899046 chr1:155899036-155899047 chr1:155898883-155898895
11	STAT3	chr1:155899001-155899021	MCF10A-Er-Src	breast:	n/a	n/a
12	JUN	chr1:155898936-155899129	K562	blood:	n/a	chr1:155899039-155899046
13	FOS	chr1:155898833-155899415	MCF10A-Er-Src	breast:	n/a	chr1:155899039-155899046 chr1:155899036-155899047 chr1:155898883-155898895
14	POLR2A	chr1:155898832-155899243	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:155898922-155899281	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:155898862-155899225	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr1:155898870-155899265	PFSK-1	brain:	n/a	n/a
18	STAT3	chr1:155899016-155899137	MCF10A-Er-Src	breast:	n/a	n/a
19	JUND	chr1:155898912-155899187	K562	blood:	n/a	chr1:155899039-155899046
20	JUND	chr1:155898859-155899208	Hela-S3	cervix:	n/a	chr1:155899039-155899046 chr1:155898883-155898895
21	FOS	chr1:155898867-155899203	HUVEC	blood vessel:	n/a	chr1:155899039-155899046 chr1:155899036-155899047 chr1:155898883-155898895
22	FOS	chr1:155898851-155899255	MCF10A-Er-Src	breast:	n/a	chr1:155899039-155899046 chr1:155899036-155899047 chr1:155898883-155898895
23	GATA2	chr1:155898916-155899266	HUVEC	blood vessel:	n/a	chr1:155899069-155899076 chr1:155899039-155899048 chr1:155899069-155899076 chr1:155899062-155899083 chr1:155899064-155899080 chr1:155899069-155899076

No.	Distal block	Cell Line	Cell type
1	chr1:155893064..155900339-chr1:155902644..155906758,10	MCF-7	breast:
2	chr1:155897781..155902008-chr1:155946105..155951194,6	K562	blood:
3	chr1:155897781..155900441-chr1:155946771..155949716,3	K562	blood:
4	chr1:155898876..155902845-chr1:155952494..155955112,4	K562	blood:
5	chr1:155898778..155900768-chr1:155910276..155912897,2	K562	blood:

Variant related genes	Relation type
SCARNA4	TF binding region
KIAA0907	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000173080	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10796955	0.80[CHB][hapmap]
rs11264422	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12024880	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027412	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563627	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1749410	0.82[ASN][1000 genomes]
rs1889532	0.80[CHB][hapmap]
rs2993207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4661151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4661175	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4661218	0.80[CHB][hapmap]
rs488079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490498	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639398	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656247	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656737	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670523	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs729022	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7517204	0.82[ASN][1000 genomes]
rs7538214	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs822504	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs822505	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs822508	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs822509	0.82[ASN][1000 genomes]
rs928596	0.80[CHB][hapmap]

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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs539602	RIT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155881800-155899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:155881800-155900600	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:155881800-155901200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:155881800-155901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:155882000-155899400	Strong transcription	Fetal Intestine Large	intestine
6	chr1:155882000-155899800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:155882000-155900000	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:155882000-155900000	Strong transcription	Liver	Liver
9	chr1:155882000-155900200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:155882000-155900400	Strong transcription	Primary B cells from cord blood	blood
11	chr1:155882000-155900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:155882000-155900600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:155882000-155900600	Strong transcription	Placenta	Placenta
14	chr1:155882000-155900600	Strong transcription	Fetal Stomach	stomach
15	chr1:155882000-155900600	Strong transcription	Left Ventricle	heart
16	chr1:155882000-155900800	Strong transcription	Thymus	Thymus
17	chr1:155882000-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:155882000-155901400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:155882000-155901400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:155882200-155900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:155882200-155900600	Strong transcription	Fetal Thymus	thymus
22	chr1:155882200-155901000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:155882200-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:155882200-155901200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:155882200-155901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:155882200-155901400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:155882200-155901400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:155882200-155903000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:155882400-155900000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:155882400-155900000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:155882400-155900000	Strong transcription	Adipose Nuclei	Adipose
32	chr1:155882400-155900200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:155882600-155900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:155882600-155900200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:155882600-155901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:155882600-155901600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:155882800-155899400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:155882800-155899400	Strong transcription	GM12878-XiMat	blood
39	chr1:155882800-155901400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:155882800-155901600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:155882800-155902600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr1:155883000-155899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:155883000-155899800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:155883000-155900000	Strong transcription	Primary T cells from cord blood	blood
45	chr1:155883000-155900000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:155883000-155900200	Strong transcription	Brain Anterior Caudate	brain
47	chr1:155883000-155900400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:155883000-155900400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:155883000-155900600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:155883000-155902200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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