Variant report

Variant	rs3790661
Chromosome Location	chr1:165868496-165868497
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	TCF12	chr1:165867759-165868755	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:165864447-165870499	IMR90	lung:	n/a	n/a
4	JUND	chr1:165867846-165868712	SK-N-SH	brain:	n/a	chr1:165868354-165868365
5	FOSL2	chr1:165867853-165868669	SK-N-SH	brain:	n/a	chr1:165868354-165868365
6	CTCF	chr1:165868420-165868570	HBMEC	blood vessel:	n/a	n/a
7	JUND	chr1:165867833-165868662	SK-N-SH	brain:	n/a	chr1:165868354-165868365
8	EP300	chr1:165867974-165868517	SK-N-SH	brain:	n/a	n/a
9	MYC	chr1:165867999-165868531	MCF10A-Er-Src	breast:	n/a	chr1:165868230-165868246
10	TEAD4	chr1:165867894-165868667	SK-N-SH	brain:	n/a	n/a
11	USF1	chr1:165868264-165868510	A549	lung:	n/a	n/a
12	GATA3	chr1:165867883-165868648	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr1:165867801-165868699	SK-N-SH	brain:	n/a	n/a
14	USF2	chr1:165868334-165868521	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr1:165867866-165868683	IMR90	lung:	n/a	n/a
16	MAZ	chr1:165865258-165869632	IMR90	lung:	n/a	chr1:165865613-165865623 chr1:165869315-165869324 chr1:165868230-165868246
17	POLR2A	chr1:165867984-165868558	SK-N-SH	brain:	n/a	n/a
18	RCOR1	chr1:165866753-165869463	IMR90	lung:	n/a	n/a
19	GATA3	chr1:165867803-165868744	SK-N-SH	brain:	n/a	n/a
20	USF1	chr1:165868164-165868548	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr1:165867921-165868573	U87	brain:	n/a	n/a
22	USF1	chr1:165868207-165868497	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr1:165868400-165868550	HPF	lung:	n/a	n/a
24	FOSL2	chr1:165868022-165868557	SK-N-SH	brain:	n/a	chr1:165868354-165868365
25	MAX	chr1:165867941-165868651	SK-N-SH	brain:	n/a	chr1:165868230-165868246
26	USF1	chr1:165868053-165868643	SK-N-SH	brain:	n/a	n/a
27	SIN3AK20	chr1:165868027-165868584	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr1:165867885-165868554	HUVEC	blood vessel:	n/a	n/a
29	CHD1	chr1:165864264-165870908	IMR90	lung:	n/a	n/a
30	CTCF	chr1:165868440-165868590	HCFaa	heart:	n/a	n/a
31	CEBPB	chr1:165867792-165868715	IMR90	lung:	n/a	n/a
32	CTCF	chr1:165868440-165868590	HCPEpiC	choroid plexus:	n/a	n/a
33	MAX	chr1:165867953-165868646	SK-N-SH	brain:	n/a	chr1:165868230-165868246
34	PBX3	chr1:165867903-165868672	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr1:165867765-165869294	K562	blood:	n/a	n/a
36	PBX3	chr1:165867858-165868564	SK-N-SH	brain:	n/a	n/a
37	JUND	chr1:165867868-165868662	SK-N-SH	brain:	n/a	chr1:165868354-165868365
38	TEAD4	chr1:165867904-165868561	SK-N-SH	brain:	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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1061771	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918307	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663840	1.00[EUR][1000 genomes]
rs2153261	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2153262	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2185267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2275432	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2349109	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3748701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790657	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790662	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790663	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666697	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681761	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73031470	1.00[EUR][1000 genomes];1.00[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
rs3790661	HMGA2	trans	lymphoblastoid	seeQTL

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	chr1:165859400-165871200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr1:165859400-165880200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:165859400-165880400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:165859400-165880600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:165859400-165880600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:165859600-165870200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:165859600-165870800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:165859600-165880600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:165859800-165870600	Strong transcription	Fetal Brain Female	brain
27	chr1:165860000-165880200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr1:165860400-165869200	Strong transcription	Brain Germinal Matrix	brain
29	chr1:165860400-165870400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:165861600-165869800	Weak transcription	Fetal Brain Male	brain
31	chr1:165861800-165869400	Weak transcription	Ovary	ovary
32	chr1:165862000-165871800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:165862400-165871800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:165863800-165868800	Strong transcription	Fetal Intestine Small	intestine
35	chr1:165864000-165870000	Enhancers	Left Ventricle	heart
36	chr1:165864200-165869400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:165864200-165870000	Enhancers	Right Ventricle	heart
38	chr1:165864200-165870800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr1:165864600-165869200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:165864600-165869400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:165864600-165872000	Weak transcription	Primary B cells from cord blood	blood
42	chr1:165865000-165870600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:165865000-165872600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:165865800-165868800	Weak transcription	Lung	lung
45	chr1:165866000-165871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:165866400-165868800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:165866400-165868800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:165866400-165869000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:165866400-165869200	Weak transcription	Liver	Liver
50	chr1:165866400-165869800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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