Variant report

Variant	rs3821712
Chromosome Location	chr3:141205185-141205186
allele	C/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	POLR2A	chr3:141204645-141205785	U87	brain:	n/a	n/a
2	SP1	chr3:141204674-141205275	A549	lung:	n/a	n/a
3	FOS	chr3:141204796-141205222	MCF10A-Er-Src	breast:	n/a	chr3:141205189-141205198
4	RCOR1	chr3:141205160-141205236	K562	blood:	n/a	n/a
5	SP1	chr3:141205113-141205748	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:141205155-141205737	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr3:141204940-141207413	IMR90	lung:	n/a	chr3:141204946-141204961
8	POLR2A	chr3:141204567-141206988	HepG2	liver:	n/a	n/a
9	STAT3	chr3:141204831-141205600	MCF10A-Er-Src	breast:	n/a	n/a
10	MAZ	chr3:141204422-141207328	IMR90	lung:	n/a	chr3:141204946-141204955 chr3:141205187-141205197 chr3:141206243-141206252
11	POLR2A	chr3:141204583-141206968	HUVEC	blood vessel:	n/a	n/a
12	SPI1	chr3:141204330-141205241	HL-60	blood:	n/a	chr3:141204599-141204612 chr3:141204601-141204610 chr3:141204598-141204611 chr3:141204602-141204609
13	STAT3	chr3:141204836-141205653	MCF10A-Er-Src	breast:	n/a	n/a
14	MAZ	chr3:141205035-141205224	HepG2	liver:	n/a	chr3:141205187-141205197
15	TCF12	chr3:141204664-141206919	A549	lung:	n/a	n/a
16	ZNF263	chr3:141205093-141206085	HEK293-T-REx	kidney:	n/a	n/a
17	TEAD4	chr3:141204798-141205291	HepG2	liver:	n/a	n/a
18	TBP	chr3:141204847-141206902	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUND	chr3:141204958-141205669	H1-hESC	embryonic stem cell:	n/a	chr3:141205189-141205198
20	POLR2A	chr3:141204569-141206776	HUVEC	blood vessel:	n/a	n/a
21	REST	chr3:141204618-141205797	A549	lung:	n/a	n/a
22	POLR2A	chr3:141204295-141207151	HUVEC	blood vessel:	n/a	n/a
23	E2F4	chr3:141204913-141206090	MCF10A-Er-Src	breast:	n/a	chr3:141206063-141206073 chr3:141205535-141205542 chr3:141205534-141205546 chr3:141205535-141205542 chr3:141205535-141205542
24	POLR2A	chr3:141204979-141207418	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr3:141204398-141205364	HUVEC	blood vessel:	n/a	chr3:141205189-141205198
26	SIN3A	chr3:141205148-141207244	H1-hESC	embryonic stem cell:	n/a	chr3:141206666-141206677 chr3:141205839-141205852 chr3:141206503-141206516 chr3:141206445-141206456 chr3:141206451-141206460
27	FOS	chr3:141204845-141205240	MCF10A-Er-Src	breast:	n/a	chr3:141205189-141205198
28	SP1	chr3:141204558-141205810	A549	lung:	n/a	n/a
29	POLR2A	chr3:141204830-141205267	HUVEC	blood vessel:	n/a	n/a
30	STAT3	chr3:141204833-141205554	MCF10A-Er-Src	breast:	n/a	n/a
31	FOSL2	chr3:141204685-141205730	A549	lung:	n/a	chr3:141205189-141205198
32	POLR2A	chr3:141204651-141205779	U87	brain:	n/a	n/a
33	RFX5	chr3:141204947-141206033	Hela-S3	cervix:	n/a	n/a
34	EGR1	chr3:141205151-141206908	HCT-116	colon:	n/a	chr3:141205358-141205380 chr3:141206268-141206282 chr3:141206111-141206121 chr3:141206108-141206121 chr3:141205186-141205196 chr3:141205764-141205778 chr3:141206107-141206122 chr3:141206108-141206121
35	POLR2A	chr3:141204727-141205196	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr3:141204748-141208045	SK-N-SH	brain:	n/a	chr3:141204946-141204961
37	POLR2A	chr3:141204793-141207037	H1-hESC	embryonic stem cell:	n/a	n/a
38	FOS	chr3:141204775-141205582	MCF10A-Er-Src	breast:	n/a	chr3:141205189-141205198
39	GATA2	chr3:141204305-141205231	HUVEC	blood vessel:	n/a	chr3:141204791-141204800 chr3:141204791-141204798 chr3:141204788-141204798 chr3:141204791-141204798 chr3:141204790-141204800 chr3:141204784-141204805 chr3:141204791-141204798
40	MAFK	chr3:141204664-141205191	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141204551..141207938-chr3:141241119..141245308,6	MCF-7	breast:
2	chr3:141194536..141196661-chr3:141202566..141205649,3	K562	blood:
3	chr3:141189849..141195094-chr3:141204829..141208801,7	MCF-7	breast:
4	chr3:141203440..141205280-chr3:141224808..141226638,2	K562	blood:
5	chr3:141085187..141087816-chr3:141204878..141206678,4	MCF-7	breast:
6	chr3:141205080..141206779-chr6:76458156..76460847,2	MCF-7	breast:
7	chr3:141085737..141089975-chr3:141204779..141207356,5	K562	blood:

Variant related genes	Relation type
RASA2	TF binding region
ENSG00000196586	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000250170	Chromatin interaction
ENSG00000215606	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11711375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916906	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11917587	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062809	0.81[EUR][1000 genomes]
rs13069717	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1366042	0.96[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1493209	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16851435	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2172471	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs295320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295323	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35711802	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440015	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6763498	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776003	0.89[CEU][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6785874	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6800122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6808837	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7627807	0.88[JPT][hapmap]
rs7632308	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7643837	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289631	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9813177	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9851256	0.87[CEU][hapmap]
rs9878347	0.94[JPT][hapmap]
rs9879503	0.94[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3423260	chr3:141204887-141207435	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3821712	RASA2	cis	cerebellum	SCAN
rs3821712	ATP1B3	cis	cerebellum	SCAN
rs3821712	RASA2	cis	parietal	SCAN
rs3821712	RASA2	Cis_1M	lymphoblastoid	RTeQTL
rs3821712	GK5	cis	parietal	SCAN
rs3821712	ZBTB38	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141201200-141205400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:141201400-141205400	Enhancers	Placenta	Placenta
3	chr3:141203000-141205600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:141203400-141205600	Enhancers	Lung	lung
5	chr3:141203800-141205200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:141203800-141205200	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:141203800-141205200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:141203800-141205200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:141203800-141205400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:141204000-141205400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:141204000-141205400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:141204200-141205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:141204200-141205200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:141204200-141205200	Enhancers	Fetal Intestine Large	intestine
15	chr3:141204200-141205200	Enhancers	Dnd41	blood
16	chr3:141204200-141205600	Flanking Active TSS	HUVEC	blood vessel
17	chr3:141204200-141205800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr3:141204200-141208000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr3:141204400-141205200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:141204400-141205200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:141204400-141205200	Enhancers	HSMM	muscle
22	chr3:141204400-141205800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr3:141204600-141205200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:141204600-141205200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:141204600-141205200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:141204600-141205200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:141204600-141205200	Enhancers	Brain Hippocampus Middle	brain
28	chr3:141204600-141205400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:141204600-141205400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:141204600-141205400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:141204600-141205400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr3:141204600-141205400	Enhancers	Fetal Thymus	thymus
33	chr3:141204600-141205400	Enhancers	Left Ventricle	heart
34	chr3:141204600-141205400	Enhancers	Stomach Mucosa	stomach
35	chr3:141204600-141205400	Flanking Active TSS	A549	lung
36	chr3:141204600-141205400	Enhancers	HSMMtube	muscle
37	chr3:141204600-141205600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr3:141204600-141205600	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr3:141204600-141205600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr3:141204600-141205600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:141204600-141205600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr3:141204600-141205600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:141204600-141205600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr3:141204600-141205600	Flanking Active TSS	NHDF-Ad	bronchial
45	chr3:141204600-141205600	Flanking Active TSS	NHEK	skin
46	chr3:141204600-141205600	Flanking Active TSS	Osteobl	bone
47	chr3:141204600-141205800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:141204600-141205800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:141204800-141205200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr3:141204800-141205200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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