Variant report

Variant	rs1978053
Chromosome Location	chr1:174985202-174985203
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	chr1:174985150-174985293	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:174984193-174985406	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:174984978-174985278	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174967096..174970659-chr1:174981028..174985682,6	MCF-7	breast:
2	chr1:174982973..174985491-chr1:174991343..174993295,2	MCF-7	breast:
3	chr1:174967695..174969619-chr1:174984996..174987018,2	MCF-7	breast:
4	chr1:174845505..174847927-chr1:174983132..174985506,2	K562	blood:

Variant related genes	Relation type
MRPS14	TF binding region
ENSG00000116161	Chromatin interaction
ENSG00000120333	Chromatin interaction
ENSG00000206659	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1046439	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1801791	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984418	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2105949	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2187939	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285208	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2285210	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301507	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35996757	0.84[ASN][1000 genomes]
rs6425309	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6425310	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6669560	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514888	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv947512	chr1:174984818-175000909	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174970000-174991800	Weak transcription	Stomach Mucosa	stomach
2	chr1:174970800-174986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:174971000-174991600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:174973000-174990600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:174973200-174987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:174973200-174987800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:174973200-174988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:174973600-174987800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:174973600-174988200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:174973600-174990400	Strong transcription	Primary T cells from cord blood	blood
11	chr1:174973800-174987600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:174973800-174987800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr1:174973800-174987800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:174973800-174987800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:174973800-174987800	Strong transcription	Fetal Intestine Large	intestine
16	chr1:174973800-174987800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:174973800-174988200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr1:174973800-174988400	Strong transcription	Fetal Thymus	thymus
19	chr1:174973800-174988800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr1:174973800-174988800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:174973800-174989800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:174974000-174987800	Strong transcription	Liver	Liver
23	chr1:174974000-174988200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:174974000-174988400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:174974200-174987600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:174974200-174987800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:174974200-174987800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:174974200-174987800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:174974200-174987800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:174974200-174987800	Strong transcription	A549	lung
31	chr1:174974200-174987800	Strong transcription	HMEC	breast
32	chr1:174974200-174987800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:174974200-174988200	Strong transcription	Thymus	Thymus
34	chr1:174974200-174988400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:174974200-174988400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:174974200-174988800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:174974200-174990200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:174974400-174985600	Strong transcription	Adipose Nuclei	Adipose
39	chr1:174974400-174987600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:174974400-174987800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:174974400-174987800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:174974400-174987800	Strong transcription	Placenta	Placenta
43	chr1:174974400-174987800	Strong transcription	HepG2	liver
44	chr1:174974400-174988400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:174974600-174987000	Strong transcription	HSMM	muscle
46	chr1:174974600-174987400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:174974600-174987800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:174974800-174989400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:174975200-174988200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:174975800-174987600	Strong transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links