Variant report

Variant	rs2232807
Chromosome Location	chr1:171750095-171750096
allele	C/G/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	TEAD4	chr1:171749877-171750654	K562	blood:	n/a	n/a
2	POLR2A	chr1:171750056-171751316	GM15510	blood:	n/a	n/a
3	STAT3	chr1:171750064-171751197	MCF10A-Er-Src	breast:	n/a	chr1:171750340-171750348
4	MXI1	chr1:171749996-171752068	IMR90	lung:	n/a	n/a
5	BRCA1	chr1:171750076-171750990	Hela-S3	cervix:	n/a	n/a
6	ELF1	chr1:171750073-171751084	GM12878	blood:	n/a	chr1:171750768-171750780 chr1:171750645-171750657
7	SP1	chr1:171750054-171751257	HCT-116	colon:	n/a	chr1:171750619-171750631 chr1:171750620-171750629 chr1:171750619-171750631 chr1:171750620-171750634
8	REST	chr1:171749782-171751486	H1-neurons	neurons:	n/a	chr1:171750267-171750277
9	GABPA	chr1:171750091-171751405	A549	lung:	n/a	n/a
10	POLR2A	chr1:171749818-171751202	GM12892	blood:	n/a	n/a
11	ELF1	chr1:171749986-171751309	MCF-7	breast:	n/a	chr1:171750768-171750780 chr1:171750645-171750657
12	POLR2A	chr1:171749968-171751564	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:171750020-171751431	GM19099	blood:	n/a	n/a
14	SP1	chr1:171750057-171751165	HCT-116	colon:	n/a	chr1:171750619-171750631 chr1:171750620-171750629 chr1:171750619-171750631 chr1:171750620-171750634
15	POLR2A	chr1:171749822-171751083	H1-hESC	embryonic stem cell:	n/a	n/a
16	CUX1	chr1:171750074-171751133	K562	blood:	n/a	n/a
17	POLR2A	chr1:171749872-171751405	Hela-S3	cervix:	n/a	n/a
18	BACH1	chr1:171750084-171750362	K562	blood:	n/a	n/a
19	SP1	chr1:171750074-171751204	A549	lung:	n/a	chr1:171750619-171750631 chr1:171750620-171750629 chr1:171750619-171750631 chr1:171750620-171750634
20	POLR2A	chr1:171749666-171751578	K562	blood:	n/a	n/a
21	JUND	chr1:171750011-171751049	H1-hESC	embryonic stem cell:	n/a	chr1:171750440-171750450
22	POLR2A	chr1:171749989-171751122	K562	blood:	n/a	n/a
23	UBTF	chr1:171750035-171750977	K562	blood:	n/a	n/a
24	MAFK	chr1:171750033-171751143	K562	blood:	n/a	n/a
25	CEBPB	chr1:171750004-171750995	K562	blood:	n/a	chr1:171750715-171750723
26	MAX	chr1:171749999-171751320	Hela-S3	cervix:	n/a	n/a
27	RCOR1	chr1:171750068-171751167	GM12878	blood:	n/a	n/a
28	JUN	chr1:171750031-171751078	K562	blood:	n/a	chr1:171750440-171750450
29	JUND	chr1:171749878-171751367	K562	blood:	n/a	chr1:171750440-171750450
30	POLR2A	chr1:171749898-171751209	HUVEC	blood vessel:	n/a	n/a
31	MXI1	chr1:171750066-171751136	GM12878	blood:	n/a	n/a
32	MAX	chr1:171750043-171751452	A549	lung:	n/a	n/a
33	MAZ	chr1:171750021-171751089	HepG2	liver:	n/a	n/a
34	CREB1	chr1:171750081-171751116	HepG2	liver:	n/a	n/a
35	SP4	chr1:171750065-171750599	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZMIZ1	chr1:171750062-171751048	K562	blood:	n/a	n/a
37	IRF1	chr1:171749271-171751404	K562	blood:	n/a	chr1:171750714-171750723 chr1:171750617-171750631
38	E2F6	chr1:171750076-171751097	H1-hESC	embryonic stem cell:	n/a	chr1:171750399-171750410 chr1:171750714-171750723
39	NR2F2	chr1:171749658-171751562	K562	blood:	n/a	n/a
40	ATF2	chr1:171750032-171751027	GM12878	blood:	n/a	n/a
41	MAX	chr1:171749888-171751079	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:171750074-171751074	Hela-S3	cervix:	n/a	n/a
43	CBX3	chr1:171749560-171751124	K562	blood:	n/a	n/a
44	POLR2A	chr1:171750070-171751117	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr1:171750055-171750625	GM12892	blood:	n/a	n/a
46	POLR2A	chr1:171749975-171751398	PFSK-1	brain:	n/a	n/a
47	ZNF143	chr1:171750060-171750978	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr1:171750092-171750637	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr1:171749759-171751038	HCT-116	colon:	n/a	n/a
50	POLR2A	chr1:171749833-171751582	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:
2	chr1:171738907..171740950-chr1:171747822..171750244,2	MCF-7	breast:
3	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
4	chr1:155196799..155197506-chr1:171749732..171750634,2	Hela-S3	cervix:
5	chr1:171711288..171712051-chr1:171749296..171750274,2	Hela-S3	cervix:
6	chr1:171750066..171750854-chr11:94822619..94823499,2	HCT-116	colon:
7	chr1:171750001..171750811-chr11:93474122..93474719,2	NB4	blood:
8	chr1:171710046..171714350-chr1:171748592..171750523,6	K562	blood:
9	chr1:171719352..171723049-chr1:171749265..171752646,3	MCF-7	breast:
10	chr1:171735538..171739658-chr1:171748409..171750930,4	MCF-7	breast:
11	chr1:171729687..171733295-chr1:171747531..171751881,5	K562	blood:
12	chr1:171750053..171752040-chr1:171760205..171763597,3	MCF-7	breast:
13	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
14	chr1:171748445..171750403-chr1:173987079..173989780,2	MCF-7	breast:
15	chr1:171728708..171731158-chr1:171748251..171750478,2	MCF-7	breast:
16	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:
17	chr1:171749924..171750607-chr10:105211765..105212634,2	HCT-116	colon:
18	chr1:171734176..171737844-chr1:171748206..171752284,5	K562	blood:
19	chr1:171724145..171725831-chr1:171749285..171750823,2	K562	blood:

Variant related genes	Relation type
METTL13	TF binding region
ENSG00000160766	Chromatin interaction
ENSG00000166012	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000253060	Chromatin interaction
ENSG00000234699	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000138172	Chromatin interaction
ENSG00000232261	Chromatin interaction
ENSG00000271459	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000149218	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1045456	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489252	0.82[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913680	0.82[AFR][1000 genomes]
rs10913683	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12090298	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs12091786	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565176	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12567851	0.86[EUR][1000 genomes]
rs12730717	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12750330	0.87[EUR][1000 genomes]
rs12753043	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17596025	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17596081	0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17649609	0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs17650310	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.90[EUR][1000 genomes]
rs1801898	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143369	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181216	0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2223602	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2232813	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232819	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232825	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294718	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236894	0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs236897	0.85[EUR][1000 genomes]
rs236898	0.85[EUR][1000 genomes]
rs236899	0.85[EUR][1000 genomes]
rs236900	0.86[EUR][1000 genomes]
rs34320898	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35400839	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35631282	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35674909	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35882887	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35930163	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36080557	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3891278	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.90[EUR][1000 genomes]
rs56365362	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656852	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.97[EUR][1000 genomes]
rs6675708	0.97[EUR][1000 genomes]
rs6681322	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6687624	0.90[JPT][hapmap]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7522582	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536142	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9970108	0.83[YRI][hapmap]
rs9970212	0.90[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv1802105	chr1:171749558-171751236	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1802411	chr1:171749665-171751051	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv522889	chr1:171749665-171755071	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2232807	RHOA	trans	parietal	SCAN
rs2232807	MAEL	cis	parietal	SCAN
rs2232807	DUSP27	cis	parietal	SCAN
rs2232807	C1orf9	cis	parietal	SCAN
rs2232807	PIGC	cis	parietal	SCAN
rs2232807	VAMP4	cis	cerebellum	SCAN
rs2232807	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs2232807	METTL13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171749000-171750200	Flanking Active TSS	Dnd41	blood
2	chr1:171749400-171750200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:171749400-171750200	Flanking Active TSS	K562	blood
4	chr1:171749600-171750200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr1:171749600-171750200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr1:171749600-171750200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:171749600-171750200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:171749600-171750200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:171749600-171750200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:171749600-171750200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:171749600-171750200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:171749600-171750200	Flanking Active TSS	Fetal Thymus	thymus
13	chr1:171749600-171750200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr1:171749600-171750200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr1:171749600-171750200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr1:171749600-171750200	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:171749600-171750400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr1:171749600-171750400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr1:171749600-171751200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:171749600-171751400	Active TSS	Brain Anterior Caudate	brain
21	chr1:171749600-171751400	Active TSS	Fetal Heart	heart
22	chr1:171749600-171751400	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:171749600-171751600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:171749600-171751600	Active TSS	Brain Substantia Nigra	brain
25	chr1:171749600-171751800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:171749600-171751800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:171749600-171751800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:171749600-171751800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:171749600-171751800	Active TSS	Fetal Kidney	kidney
30	chr1:171749600-171752000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:171749600-171752000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr1:171749600-171752200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:171749600-171752400	Active TSS	Rectal Smooth Muscle	rectum
34	chr1:171749800-171750200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:171749800-171750200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:171749800-171750200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:171749800-171750200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr1:171749800-171750200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:171749800-171750200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr1:171749800-171750200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:171749800-171750200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:171749800-171750200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr1:171749800-171750200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:171749800-171750200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr1:171749800-171750200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:171749800-171750200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:171749800-171750200	Flanking Active TSS	Fetal Lung	lung
48	chr1:171749800-171750200	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr1:171749800-171750200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:171749800-171750200	Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links