Variant report

Variant	rs1578992
Chromosome Location	chr1:212211174-212211175
allele	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	WRNIP1	chr1:212211063-212211744	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:212210881-212211756	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr1:212211166-212211815	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212207393..212212126-chr1:212456103..212460187,5	K562	blood:

Variant related genes	Relation type
INTS7	TF binding region
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10779568	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863939	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119839	0.82[ASN][1000 genomes]
rs1578993	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806360	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2014029	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2130503	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2248191	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2251398	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2358386	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2358440	0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs2788133	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2788139	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2788140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs2808385	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2808392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2884428	0.91[JPT][hapmap]
rs2884457	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970592	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2970599	0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs2970601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2993528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2993529	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2993531	0.86[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2993533	0.91[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2993541	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2993544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3009985	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3010003	0.91[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes]
rs3010004	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs3010023	0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3010024	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3738449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657728	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6670844	0.82[ASN][1000 genomes]
rs7522330	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7550754	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1578992	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212207200-212211400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:212207400-212211200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:212207600-212211400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:212207600-212211400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:212207800-212211400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:212208400-212211200	Active TSS	Fetal Thymus	thymus
7	chr1:212209200-212212000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:212209400-212217800	Weak transcription	Small Intestine	intestine
9	chr1:212209600-212226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:212209600-212253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:212209800-212211200	Flanking Active TSS	HUVEC	blood vessel
12	chr1:212209800-212211400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:212209800-212211600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:212209800-212214000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:212210000-212211200	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr1:212210200-212211200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:212210200-212212000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:212210200-212213800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:212210200-212214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:212210400-212211200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:212210400-212211200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:212210400-212211600	Enhancers	Fetal Lung	lung
23	chr1:212210400-212211600	Flanking Active TSS	HepG2	liver
24	chr1:212210400-212214000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:212210400-212214000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:212210400-212214000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:212210400-212223600	Weak transcription	HSMM	muscle
28	chr1:212210400-212227400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:212210400-212228800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:212210400-212228800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:212210400-212228800	Weak transcription	Fetal Intestine Large	intestine
32	chr1:212210600-212211200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:212210600-212211200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:212210600-212211200	Flanking Active TSS	Hela-S3	cervix
35	chr1:212210600-212211400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212210600-212211400	Enhancers	Osteobl	bone
37	chr1:212210600-212211600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:212210600-212211800	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:212210600-212212400	Transcr. at gene 5' and 3'	K562	blood
40	chr1:212210600-212213800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:212210600-212213800	Weak transcription	Primary T cells from cord blood	blood
42	chr1:212210600-212214000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:212210600-212214000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:212210600-212214600	Transcr. at gene 5' and 3'	Dnd41	blood
45	chr1:212210600-212215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:212210600-212227400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:212210600-212229200	Weak transcription	Fetal Brain Female	brain
48	chr1:212210800-212211200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:212210800-212211200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:212210800-212211200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links