Variant report

Variant	rs3790654
Chromosome Location	chr1:165862264-165862265
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	chr1:165862041-165862633	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:165862052-165862499	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165598675..165601057-chr1:165860826..165863471,2	K562	blood:

Variant related genes	Relation type
UCK2	TF binding region
ENSG00000143198	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12060526	0.87[GIH][hapmap];0.89[JPT][hapmap]
rs12118019	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12119028	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12569109	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1663841	0.92[ASN][1000 genomes]
rs16852447	0.82[AMR][1000 genomes]
rs3790668	0.95[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790669	0.90[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3790670	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3790674	0.91[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4656464	0.92[ASN][1000 genomes]
rs4656465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656467	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4657489	0.85[ASW][hapmap];0.86[CHD][hapmap]
rs475558	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs504436	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs514163	0.91[CEU][hapmap];0.91[GIH][hapmap]
rs530717	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs576213	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426943	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661905	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6682285	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687465	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7520107	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7547020	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9787031	0.81[AMR][1000 genomes];0.80[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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3790654	ITLN2	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165853400-165864600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:165854000-165869600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:165854400-165865400	Weak transcription	Fetal Lung	lung
4	chr1:165854600-165883000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:165855000-165863800	Weak transcription	HUVEC	blood vessel
6	chr1:165856400-165869600	Weak transcription	Fetal Kidney	kidney
7	chr1:165856600-165878800	Weak transcription	Small Intestine	intestine
8	chr1:165857800-165863600	Weak transcription	Stomach Mucosa	stomach
9	chr1:165857800-165865800	Weak transcription	Colonic Mucosa	Colon
10	chr1:165858200-165881200	Strong transcription	Dnd41	blood
11	chr1:165858400-165862400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:165858400-165870000	Strong transcription	K562	blood
13	chr1:165858400-165881000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:165858600-165866800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:165858600-165872000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:165858600-165872600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:165859000-165866200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:165859000-165881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:165859200-165862400	Strong transcription	Fetal Intestine Small	intestine
21	chr1:165859200-165862600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:165859200-165862800	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr1:165859200-165864600	Strong transcription	NHEK	skin
24	chr1:165859200-165866000	Strong transcription	GM12878-XiMat	blood
25	chr1:165859200-165870400	Strong transcription	Fetal Stomach	stomach
26	chr1:165859200-165871000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr1:165859200-165871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:165859200-165878000	Strong transcription	Hela-S3	cervix
29	chr1:165859200-165880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:165859200-165881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:165859400-165862400	Strong transcription	Aorta	Aorta
32	chr1:165859400-165862800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:165859400-165864200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:165859400-165864800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:165859400-165866800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:165859400-165868000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:165859400-165868400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:165859400-165868400	Strong transcription	HepG2	liver
39	chr1:165859400-165871200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:165859600-165864200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:165859600-165870200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:165859600-165870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:165859800-165862400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:165859800-165862400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:165859800-165864600	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links