Variant report

Variant	rs12087573
Chromosome Location	chr1:171770432-171770433
allele	C/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	USF2	chr1:171770350-171770766	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr1:171770340-171770490	GM12865	blood:	n/a	n/a
3	CTCF	chr1:171770174-171771278	SK-N-SH	brain:	n/a	chr1:171770733-171770741 chr1:171770299-171770320 chr1:171770730-171770751 chr1:171770728-171770746 chr1:171770729-171770745
4	BHLHE40	chr1:171770362-171770904	K562	blood:	n/a	n/a
5	CTCF	chr1:171770300-171770450	HFF	foreskin:	n/a	n/a
6	SMC3	chr1:171770422-171770963	K562	blood:	n/a	chr1:171770730-171770744
7	SMC3	chr1:171770326-171771215	SK-N-SH	brain:	n/a	chr1:171770730-171770744
8	RAD21	chr1:171770429-171771113	MCF-7	breast:	n/a	chr1:171770574-171770583 chr1:171770729-171770748 chr1:171770731-171770738
9	ZNF143	chr1:171770357-171770937	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:171770425-171770496	Lung_OC	lung:	n/a	n/a
11	CTCF	chr1:171770314-171771288	HCT-116	colon:	n/a	chr1:171770733-171770741 chr1:171770730-171770751 chr1:171770728-171770746 chr1:171770729-171770745
12	POLR2A	chr1:171769990-171770784	GM12878	blood:	n/a	n/a
13	CTCF	chr1:171770147-171771845	A549	lung:	n/a	chr1:171770733-171770741 chr1:171770299-171770320 chr1:171770730-171770751 chr1:171770728-171770746 chr1:171770729-171770745
14	RAD21	chr1:171770428-171771140	HCT-116	colon:	n/a	chr1:171770574-171770583 chr1:171770729-171770748 chr1:171770731-171770738
15	RAD21	chr1:171770002-171771149	SK-N-SH	brain:	n/a	chr1:171770574-171770583 chr1:171770308-171770317 chr1:171770729-171770748 chr1:171770731-171770738
16	CTCF	chr1:171770417-171770496	GM10266	blood:	n/a	n/a
17	POLR2A	chr1:171770432-171770512	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171768938..171770911-chr1:171953198..171954740,2	MCF-7	breast:
2	chr1:171769381..171771260-chr1:171953518..171955015,12	MCF-7	breast:
3	chr1:171770266..171771184-chr1:171819765..171820356,3	MCF-7	breast:
4	chr1:171770288..171771178-chr1:171954010..171954686,4	K562	blood:
5	chr1:171769639..171771616-chr1:171952138..171953508,27	MCF-7	breast:
6	chr1:171770037..171771242-chr1:171953555..171955020,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213060	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10913650	1.00[AMR][1000 genomes]
rs10913759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10913898	0.85[YRI][hapmap]
rs12062177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064937	0.85[YRI][hapmap]
rs12087804	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089309	0.85[YRI][hapmap]
rs12093518	0.85[YRI][hapmap]
rs12094855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232815	0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535018	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7554281	0.85[YRI][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	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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:171765600-171770800	Weak transcription	Hela-S3	cervix
5	chr1:171766000-171772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:171766600-171770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:171766600-171774600	Weak transcription	Ovary	ovary
15	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
17	chr1:171766600-171774800	Weak transcription	HepG2	liver
18	chr1:171766800-171771800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:171766800-171772800	Weak transcription	Right Ventricle	heart
20	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:171767000-171770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:171767000-171770800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:171767000-171771600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:171767000-171774600	Weak transcription	K562	blood
26	chr1:171767000-171774800	Weak transcription	Osteobl	bone
27	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:171767000-171778600	Weak transcription	NHEK	skin
29	chr1:171767200-171774600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:171767200-171774800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:171767200-171774800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:171767200-171777600	Weak transcription	HMEC	breast
33	chr1:171767400-171770800	Weak transcription	A549	lung
34	chr1:171767400-171771000	Weak transcription	Fetal Brain Female	brain
35	chr1:171767400-171771400	Weak transcription	NHLF	lung
36	chr1:171767400-171771600	Weak transcription	Dnd41	blood
37	chr1:171767400-171773600	Weak transcription	HUVEC	blood vessel
38	chr1:171767400-171774600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:171767400-171774800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:171767400-171774800	Weak transcription	Psoas Muscle	Psoas
41	chr1:171767400-171775000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:171767400-171777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:171767600-171770800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:171767600-171772000	Weak transcription	Lung	lung
45	chr1:171767600-171774800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:171767600-171774800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:171767600-171775000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:171767800-171770600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:171767800-171770600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:171767800-171770600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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