Variant report

Variant	rs1627630
Chromosome Location	chr1:155828911-155828912
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	BHLHE40	chr1:155828858-155830514	GM12878	blood:	n/a	n/a
2	TBP	chr1:155828802-155829258	Hela-S3	cervix:	n/a	n/a
3	SP1	chr1:155828861-155829351	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF384	chr1:155828194-155829192	K562	blood:	n/a	n/a
5	NR2F2	chr1:155828677-155829542	K562	blood:	n/a	n/a
6	STAT3	chr1:155828863-155829360	MCF10A-Er-Src	breast:	n/a	n/a
7	GTF3C2	chr1:155828250-155829160	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr1:155828712-155829025	ECC-1	luminal epithelium:	n/a	chr1:155828813-155828824
9	ZNF384	chr1:155828085-155829223	GM12878	blood:	n/a	n/a
10	JUN	chr1:155828448-155831227	K562	blood:	n/a	chr1:155830459-155830472 chr1:155829792-155829803
11	REST	chr1:155828738-155831562	H1-neurons	neurons:	n/a	chr1:155830066-155830079 chr1:155829006-155829020 chr1:155830399-155830412
12	STAT5A	chr1:155828806-155830621	GM12878	blood:	n/a	chr1:155829998-155830010 chr1:155829965-155829977 chr1:155829969-155829981
13	POLR2A	chr1:155828760-155830864	U87	brain:	n/a	n/a
14	POLR2A	chr1:155828731-155829203	GM12878	blood:	n/a	n/a
15	FOS	chr1:155828774-155829291	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:155828867-155829244	HCT-116	colon:	n/a	n/a
17	MAZ	chr1:155828769-155830972	IMR90	lung:	n/a	n/a
18	ELF1	chr1:155828744-155829604	HCT-116	colon:	n/a	chr1:155829213-155829226
19	ATF2	chr1:155828867-155829402	GM12878	blood:	n/a	n/a
20	FOXM1	chr1:155828772-155829688	GM12878	blood:	n/a	n/a
21	TAF1	chr1:155828817-155829165	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:155828820-155830931	SK-N-SH	brain:	n/a	n/a
23	POU2F2	chr1:155828079-155829164	GM12878	blood:	n/a	chr1:155828206-155828227
24	MYBL2	chr1:155828904-155829396	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:155828882-155829249	K562	blood:	n/a	n/a
26	E2F4	chr1:155828717-155829239	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr1:155828817-155829379	PFSK-1	brain:	n/a	n/a
28	STAT3	chr1:155828754-155829336	MCF10A-Er-Src	breast:	n/a	n/a
29	SP1	chr1:155828862-155829441	A549	lung:	n/a	n/a
30	CEBPB	chr1:155828724-155828999	A549	lung:	n/a	chr1:155828813-155828824
31	MXI1	chr1:155828036-155831184	SK-N-SH	brain:	n/a	n/a
32	CEBPB	chr1:155828657-155829711	HepG2	liver:	n/a	chr1:155828813-155828824
33	POLR2A	chr1:155828910-155829585	Raji	blood:	n/a	n/a
34	KAP1	chr1:155828875-155829933	U2OS	brain:	n/a	n/a
35	TBP	chr1:155828149-155829478	GM12878	blood:	n/a	n/a
36	PML	chr1:155828739-155830841	GM12878	blood:	n/a	n/a
37	ARID3A	chr1:155828770-155829179	HepG2	liver:	n/a	n/a
38	ELF1	chr1:155828768-155829458	A549	lung:	n/a	chr1:155829213-155829226
39	WRNIP1	chr1:155828908-155829924	GM12878	blood:	n/a	n/a
40	ELF1	chr1:155828821-155829637	MCF-7	breast:	n/a	chr1:155829213-155829226
41	RUNX3	chr1:155828628-155829295	GM12878	blood:	n/a	n/a
42	NFIC	chr1:155828458-155829064	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:155828766-155830858	U87	brain:	n/a	n/a
44	ELF1	chr1:155828899-155829621	MCF-7	breast:	n/a	chr1:155829213-155829226
45	JUND	chr1:155828887-155829445	K562	blood:	n/a	n/a
46	CEBPB	chr1:155828644-155829711	K562	blood:	n/a	chr1:155828813-155828824
47	ELF1	chr1:155828878-155829434	A549	lung:	n/a	chr1:155829213-155829226
48	STAT3	chr1:155828747-155829372	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr1:155828807-155830740	GM12891	blood:	n/a	n/a
50	GABPA	chr1:155828675-155829632	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155823442..155829143-chr1:155879989..155882670,6	MCF-7	breast:
2	chr1:155821549..155823556-chr1:155827690..155829206,2	K562	blood:
3	chr1:155828536..155830676-chr1:155863027..155864768,2	MCF-7	breast:
4	chr1:155825653..155829252-chr1:155877943..155882760,5	MCF-7	breast:
5	chr1:155824896..155829386-chr1:155902844..155905236,4	MCF-7	breast:
6	chr1:155826962..155828994-chr1:155903211..155904841,2	K562	blood:
7	chr1:155827720..155829517-chr1:156180623..156183701,3	K562	blood:
8	chr1:155813223..155816752-chr1:155827638..155829227,3	K562	blood:
9	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
10	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
11	chr1:155827023..155830284-chr1:156022724..156025393,4	K562	blood:
12	chr1:155713796..155716545-chr1:155826802..155829458,2	K562	blood:

Variant related genes	Relation type
SYT11	TF binding region
GON4L	TF binding region
ENSG00000160783	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000201614	Chromatin interaction
ENSG00000234937	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000116580	Chromatin interaction
ENSG00000203761	Chromatin interaction
ENSG00000260238	Chromatin interaction
ENSG00000116586	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10796952	0.89[AMR][1000 genomes]
rs11264417	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1621690	0.84[AFR][1000 genomes]
rs1625821	1.00[AMR][1000 genomes]
rs168343	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs171168	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1749412	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749413	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749422	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1756242	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1765280	0.99[AFR][1000 genomes]
rs1765283	0.84[AFR][1000 genomes]
rs1765286	0.85[AFR][1000 genomes]
rs1886618	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2136920	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2175389	1.00[AMR][1000 genomes]
rs2363017	1.00[AMR][1000 genomes]
rs2481623	0.90[AFR][1000 genomes]
rs2485470	0.88[AFR][1000 genomes]
rs2485472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2666828	0.89[AMR][1000 genomes]
rs2686264	0.89[AMR][1000 genomes]
rs2885676	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2988999	0.89[AMR][1000 genomes]
rs348184	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348188	0.89[AMR][1000 genomes]
rs348189	0.89[AMR][1000 genomes]
rs348191	1.00[AMR][1000 genomes]
rs348193	0.89[AMR][1000 genomes]
rs348197	1.00[AMR][1000 genomes]
rs348199	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348200	1.00[AMR][1000 genomes]
rs348207	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs348208	1.00[AMR][1000 genomes]
rs348209	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35264557	0.89[AMR][1000 genomes]
rs4581273	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs492669	0.89[AMR][1000 genomes]
rs4971058	0.89[AMR][1000 genomes]
rs512551	0.93[ASW][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs540380	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs568672	1.00[AMR][1000 genomes]
rs606755	1.00[AMR][1000 genomes]
rs607036	0.81[ASW][hapmap];0.89[AMR][1000 genomes]
rs617232	0.81[ASW][hapmap];0.89[AMR][1000 genomes]
rs6427290	0.97[AFR][1000 genomes]
rs6688399	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs670787	0.89[AMR][1000 genomes]
rs708607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708609	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708613	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8179457	1.00[AMR][1000 genomes]
rs822011	0.81[AFR][1000 genomes]
rs822013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822014	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822021	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822024	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822027	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822479	0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822481	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822483	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822484	0.80[AFR][1000 genomes]
rs822485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822487	0.99[AFR][1000 genomes]
rs822492	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822496	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs822498	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822521	0.93[ASW][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs822522	1.00[AMR][1000 genomes]
rs822524	0.83[AFR][1000 genomes]
rs866603	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427219	0.89[AMR][1000 genomes]
rs9427222	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427229	0.82[AFR][1000 genomes];1.00[AMR][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	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	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155826400-155829600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:155826600-155829400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:155827000-155829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:155827000-155829200	Weak transcription	Spleen	Spleen
5	chr1:155827000-155829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:155827000-155829400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:155827000-155829400	Weak transcription	Lung	lung
8	chr1:155827200-155829000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:155827200-155829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:155827200-155829400	Weak transcription	Gastric	stomach
11	chr1:155827200-155829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:155827200-155829800	Flanking Active TSS	Dnd41	blood
13	chr1:155827400-155829000	Weak transcription	Esophagus	oesophagus
14	chr1:155827400-155829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:155828000-155829200	Active TSS	K562	blood
16	chr1:155828000-155829600	Active TSS	HepG2	liver
17	chr1:155828200-155829600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr1:155828200-155830400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:155828400-155829400	Active TSS	Stomach Smooth Muscle	stomach
20	chr1:155828400-155829400	Active TSS	A549	lung
21	chr1:155828400-155829400	Active TSS	GM12878-XiMat	blood
22	chr1:155828400-155829400	Active TSS	HSMM	muscle
23	chr1:155828400-155829400	Active TSS	NHDF-Ad	bronchial
24	chr1:155828400-155829600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:155828400-155830600	Active TSS	Psoas Muscle	Psoas
26	chr1:155828400-155831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:155828600-155829000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:155828600-155829000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:155828600-155829000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:155828600-155829000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:155828600-155829000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr1:155828600-155829000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:155828600-155829000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr1:155828600-155829000	Flanking Active TSS	Osteobl	bone
35	chr1:155828600-155829200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:155828600-155829200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr1:155828600-155829200	Active TSS	HMEC	breast
38	chr1:155828600-155829200	Active TSS	NHEK	skin
39	chr1:155828600-155829400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:155828600-155829400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:155828600-155829400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:155828600-155829400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:155828600-155829400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:155828600-155829400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:155828600-155829400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:155828600-155829400	Active TSS	Brain Germinal Matrix	brain
47	chr1:155828600-155829400	Active TSS	Duodenum Mucosa	Duodenum
48	chr1:155828600-155829400	Active TSS	Fetal Brain Female	brain
49	chr1:155828600-155829400	Active TSS	Right Ventricle	heart
50	chr1:155828600-155829400	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links