Variant report

Variant	rs3790659
Chromosome Location	chr1:165868169-165868170
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	NFIC	chr1:165867874-165868676	SK-N-SH	brain:	n/a	n/a
2	MAFK	chr1:165867961-165868458	IMR90	lung:	n/a	chr1:165868146-165868155 chr1:165868443-165868458
3	TCF12	chr1:165867759-165868755	SK-N-SH	brain:	n/a	n/a
4	FOS	chr1:165868036-165868468	MCF10A-Er-Src	breast:	n/a	chr1:165868354-165868365
5	FOS	chr1:165868086-165868421	MCF10A-Er-Src	breast:	n/a	chr1:165868354-165868365
6	POLR2A	chr1:165864447-165870499	IMR90	lung:	n/a	n/a
7	JUND	chr1:165867846-165868712	SK-N-SH	brain:	n/a	chr1:165868354-165868365
8	CTCF	chr1:165868020-165868170	HBMEC	blood vessel:	n/a	n/a
9	STAT3	chr1:165868059-165868432	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:165868024-165868433	MCF10A-Er-Src	breast:	n/a	chr1:165868354-165868365
11	FOSL2	chr1:165867853-165868669	SK-N-SH	brain:	n/a	chr1:165868354-165868365
12	MYC	chr1:165868033-165868419	MCF10A-Er-Src	breast:	n/a	chr1:165868230-165868246
13	TEAD4	chr1:165868053-165868473	ECC-1	luminal epithelium:	n/a	n/a
14	JUND	chr1:165867833-165868662	SK-N-SH	brain:	n/a	chr1:165868354-165868365
15	EP300	chr1:165867974-165868517	SK-N-SH	brain:	n/a	n/a
16	FOS	chr1:165868068-165868433	MCF10A-Er-Src	breast:	n/a	chr1:165868354-165868365
17	MYC	chr1:165867999-165868531	MCF10A-Er-Src	breast:	n/a	chr1:165868230-165868246
18	TEAD4	chr1:165867894-165868667	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr1:165867662-165868401	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:165868124-165868193	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA3	chr1:165867883-165868648	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:165867993-165868336	K562	blood:	n/a	n/a
23	STAT3	chr1:165868083-165868403	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr1:165868131-165868363	MCF10A-Er-Src	breast:	n/a	n/a
25	TCF12	chr1:165867801-165868699	SK-N-SH	brain:	n/a	n/a
26	RAD21	chr1:165867866-165868683	IMR90	lung:	n/a	n/a
27	MAZ	chr1:165865258-165869632	IMR90	lung:	n/a	chr1:165865613-165865623 chr1:165869315-165869324 chr1:165868230-165868246
28	POLR2A	chr1:165867984-165868558	SK-N-SH	brain:	n/a	n/a
29	RCOR1	chr1:165866753-165869463	IMR90	lung:	n/a	n/a
30	STAT3	chr1:165868085-165868463	MCF10A-Er-Src	breast:	n/a	n/a
31	GATA3	chr1:165867803-165868744	SK-N-SH	brain:	n/a	n/a
32	USF1	chr1:165868164-165868548	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr1:165868020-165868170	HCPEpiC	choroid plexus:	n/a	n/a
34	FOS	chr1:165868090-165868492	HUVEC	blood vessel:	n/a	chr1:165868354-165868365
35	POLR2A	chr1:165867921-165868573	U87	brain:	n/a	n/a
36	FOSL2	chr1:165868022-165868557	SK-N-SH	brain:	n/a	chr1:165868354-165868365
37	EP300	chr1:165868074-165868308	SK-N-SH_RA	brain:	n/a	n/a
38	MAX	chr1:165867941-165868651	SK-N-SH	brain:	n/a	chr1:165868230-165868246
39	USF1	chr1:165868053-165868643	SK-N-SH	brain:	n/a	n/a
40	REST	chr1:165868096-165868377	SK-N-SH	brain:	n/a	chr1:165868259-165868269
41	SIN3AK20	chr1:165868027-165868584	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr1:165868085-165868432	SK-N-SH	brain:	n/a	n/a
43	CTCF	chr1:165868060-165868210	NHDF-neo	bronchial:	n/a	n/a
44	POLR2A	chr1:165867885-165868554	HUVEC	blood vessel:	n/a	n/a
45	CHD1	chr1:165864264-165870908	IMR90	lung:	n/a	n/a
46	EP300	chr1:165868064-165868387	SK-N-SH_RA	brain:	n/a	n/a
47	CEBPB	chr1:165867792-165868715	IMR90	lung:	n/a	n/a
48	MAX	chr1:165867953-165868646	SK-N-SH	brain:	n/a	chr1:165868230-165868246
49	PBX3	chr1:165867903-165868672	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr1:165867765-165869294	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165862532..165865013-chr1:165867715..165869356,2	K562	blood:
2	chr1:165868140..165869874-chr1:165876979..165878590,2	K562	blood:

Variant related genes	Relation type
UCK2	TF binding region
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10800165	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12080800	0.88[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12125493	0.88[CEU][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2225980	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs3762365	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806333	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657486	0.89[GIH][hapmap]
rs485338	0.88[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs492467	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495529	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506813	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs536109	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544617	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519919	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543127	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3790659	USP21	cis	parietal	SCAN
rs3790659	ITLN2	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165854000-165869600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:165854600-165883000	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:165856400-165869600	Weak transcription	Fetal Kidney	kidney
4	chr1:165856600-165878800	Weak transcription	Small Intestine	intestine
5	chr1:165858200-165881200	Strong transcription	Dnd41	blood
6	chr1:165858400-165870000	Strong transcription	K562	blood
7	chr1:165858400-165881000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:165858600-165872000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:165858600-165872600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:165859000-165881000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:165859200-165870400	Strong transcription	Fetal Stomach	stomach
13	chr1:165859200-165871000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr1:165859200-165871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:165859200-165878000	Strong transcription	Hela-S3	cervix
16	chr1:165859200-165880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:165859200-165881000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:165859400-165868400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:165859400-165868400	Strong transcription	HepG2	liver
20	chr1:165859400-165871200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:165859600-165870200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:165859600-165870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:165859800-165870600	Strong transcription	Fetal Brain Female	brain
29	chr1:165860000-165880200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:165860400-165869200	Strong transcription	Brain Germinal Matrix	brain
31	chr1:165860400-165870400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:165860600-165868200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:165861600-165869800	Weak transcription	Fetal Brain Male	brain
34	chr1:165861800-165869400	Weak transcription	Ovary	ovary
35	chr1:165862000-165871800	Weak transcription	Brain Substantia Nigra	brain
36	chr1:165862400-165871800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:165863800-165868800	Strong transcription	Fetal Intestine Small	intestine
38	chr1:165864000-165870000	Enhancers	Left Ventricle	heart
39	chr1:165864200-165869400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:165864200-165870000	Enhancers	Right Ventricle	heart
41	chr1:165864200-165870800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:165864600-165869200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:165864600-165869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:165864600-165872000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:165864800-165868400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:165865000-165870600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:165865000-165872600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:165865200-165868400	Genic enhancers	A549	lung
49	chr1:165865800-165868800	Weak transcription	Lung	lung
50	chr1:165866000-165871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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