Variant report

Variant	rs1146630
Chromosome Location	chr1:76250073-76250074
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	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	MYC	chr1:76250037-76254057	K562	blood:	n/a	chr1:76250221-76250231
3	CHD2	chr1:76250045-76250634	GM12878	blood:	n/a	n/a
4	TRIM28	chr1:76249909-76250982	K562	blood:	n/a	n/a
5	MAZ	chr1:76250004-76250779	GM12878	blood:	n/a	chr1:76250221-76250231
6	IRF1	chr1:76250035-76253994	K562	blood:	n/a	chr1:76250222-76250236
7	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
8	MXI1	chr1:76250023-76251017	GM12878	blood:	n/a	n/a
9	BHLHE40	chr1:76250036-76250902	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
11	MYC	chr1:76249968-76252912	K562	blood:	n/a	chr1:76250221-76250231
12	RCOR1	chr1:76249739-76251031	K562	blood:	n/a	n/a
13	RUNX3	chr1:76249931-76250901	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:76250030-76252695	GM15510	blood:	n/a	n/a
15	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
16	TAL1	chr1:76250057-76250661	K562	blood:	n/a	n/a
17	POLR2A	chr1:76250028-76253609	K562	blood:	n/a	n/a
18	EP300	chr1:76250005-76250913	K562	blood:	n/a	n/a
19	POLR2A	chr1:76249915-76253627	Raji	blood:	n/a	n/a
20	MAZ	chr1:76250015-76251022	K562	blood:	n/a	chr1:76250221-76250231
21	RUNX3	chr1:76249979-76250991	GM12878	blood:	n/a	n/a
22	TEAD4	chr1:76250033-76250711	K562	blood:	n/a	n/a
23	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
24	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
25	EGR1	chr1:76250069-76250380	K562	blood:	n/a	chr1:76250217-76250232 chr1:76250218-76250231 chr1:76250218-76250231 chr1:76250219-76250233
26	TBL1XR1	chr1:76249814-76254171	K562	blood:	n/a	n/a
27	MAX	chr1:76250014-76251003	K562	blood:	n/a	chr1:76250221-76250231
28	NR2F2	chr1:76249890-76251158	K562	blood:	n/a	n/a
29	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
30	NFIC	chr1:76250019-76250865	GM12878	blood:	n/a	n/a
31	TEAD4	chr1:76249966-76250808	K562	blood:	n/a	n/a
32	MAX	chr1:76250038-76250280	K562	blood:	n/a	chr1:76250221-76250231
33	CBX3	chr1:76249379-76250715	K562	blood:	n/a	n/a
34	CUX1	chr1:76250032-76250590	K562	blood:	n/a	n/a
35	PML	chr1:76250044-76250875	K562	blood:	n/a	n/a
36	MYC	chr1:76249957-76253531	K562	blood:	n/a	chr1:76250221-76250231
37	IRF1	chr1:76249966-76253879	K562	blood:	n/a	chr1:76250222-76250236
38	POLR2A	chr1:76250036-76255124	K562	blood:	n/a	n/a
39	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
40	MAX	chr1:76250009-76250656	NB4	blood:	n/a	chr1:76250221-76250231
41	JUND	chr1:76250018-76250917	K562	blood:	n/a	n/a
42	GATA1	chr1:76249961-76253959	PBDE	blood:	n/a	chr1:76251865-76251874 chr1:76250253-76250263 chr1:76250253-76250260 chr1:76250251-76250260 chr1:76250246-76250267 chr1:76252359-76252372
43	POLR2A	chr1:76250055-76251100	K562	blood:	n/a	n/a
44	CHD2	chr1:76250067-76251002	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:76188658..76192178-chr1:76249968..76253902,5	MCF-7	breast:
2	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
3	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:

Variant related genes	Relation type
SNORD45A	TF binding region
RABGGTB	TF binding region
SNORD45C	TF binding region
ENSG00000117054	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11161598	0.86[ASN][1000 genomes]
rs1146598	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1146607	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1146609	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1146610	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1146617	0.86[ASN][1000 genomes]
rs1146631	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1146634	0.82[AMR][1000 genomes]
rs1146636	0.82[AMR][1000 genomes]
rs1146637	0.80[AMR][1000 genomes]
rs1146643	0.80[AMR][1000 genomes]
rs1146644	0.80[AMR][1000 genomes]
rs12092388	0.86[ASN][1000 genomes]
rs1463812	0.86[ASN][1000 genomes]
rs7552289	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1146630	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76241400-76251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:76241400-76251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:76244400-76250800	Weak transcription	HepG2	liver
4	chr1:76249200-76251200	Weak transcription	Right Atrium	heart
5	chr1:76249600-76253200	Active TSS	GM12878-XiMat	blood
6	chr1:76249800-76250200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:76249800-76250200	Enhancers	Primary B cells from peripheral blood	blood
8	chr1:76249800-76250600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:76249800-76251000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:76249800-76251200	Active TSS	K562	blood
11	chr1:76250000-76250200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:76250000-76250200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:76250000-76250400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:76250000-76250800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr1:76250000-76250800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:76250000-76250800	Active TSS	Dnd41	blood
17	chr1:76250000-76251000	Active TSS	Primary T cells from cord blood	blood

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