Variant report

Variant	rs17591640
Chromosome Location	chr1:74665060-74665061
allele	C/G
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	MYC	chr1:74664654-74665646	K562	blood:	n/a	chr1:74665356-74665366
2	CEBPB	chr1:74664885-74665549	K562	blood:	n/a	n/a
3	POLR2A	chr1:74662484-74665339	IMR90	lung:	n/a	n/a
4	SPI1	chr1:74665054-74665633	HL-60	blood:	n/a	chr1:74665321-74665330 chr1:74665136-74665149
5	CUX1	chr1:74664633-74665656	K562	blood:	n/a	n/a
6	MXI1	chr1:74663117-74665163	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:74664882-74665082	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:74664371..74665891-chr1:74684150..74685886,2	K562	blood:

Variant related genes	Relation type
LRRIQ3	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11210430	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11210433	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11210443	0.97[EUR][1000 genomes]
rs12024616	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031026	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12038237	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12043976	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402231	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12404294	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410230	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410879	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747924	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483790	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17524893	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17526617	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591703	0.84[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs17592507	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856789	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1930588	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3765654	0.96[EUR][1000 genomes]
rs9804006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970514	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004451	chr1:74107125-74874389	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv534999	chr1:74107125-74874389	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1013244	chr1:74441655-74680703	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv535001	chr1:74441655-74680703	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv871269	chr1:74484753-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv871381	chr1:74484753-74712181	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv871084	chr1:74492200-74681968	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv871456	chr1:74492200-74712181	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1008285	chr1:74517953-74705457	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1011308	chr1:74545016-74932777	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv871630	chr1:74578318-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv871909	chr1:74594901-74703758	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
16	nsv428785	chr1:74640545-74818577	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
17	nsv870486	chr1:74654182-74804833	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17591640	LRRIQ3	cis	Nerve Tibial	GTEx
rs17591640	LRRC44	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74662800-74665800	Active TSS	K562	blood
2	chr1:74663200-74665200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:74663200-74665400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr1:74663200-74665400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:74663200-74665400	Active TSS	GM12878-XiMat	blood
6	chr1:74663200-74665600	Active TSS	Right Atrium	heart
7	chr1:74663400-74665400	Active TSS	Ovary	ovary
8	chr1:74663600-74665200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:74663600-74665400	Active TSS	Primary monocytes fromperipheralblood	blood
10	chr1:74664200-74665400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:74664200-74665600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:74664200-74667400	Weak transcription	Left Ventricle	heart
13	chr1:74664200-74672000	Weak transcription	Lung	lung
14	chr1:74664200-74672000	Weak transcription	Spleen	Spleen
15	chr1:74664200-74675200	Weak transcription	Pancreas	Pancrea
16	chr1:74664400-74665200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:74664400-74665200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr1:74664400-74665600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:74664400-74665800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:74664600-74665200	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr1:74664600-74665400	Flanking Active TSS	Brain Angular Gyrus	brain
22	chr1:74664600-74665400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:74664600-74665400	Flanking Active TSS	Dnd41	blood
24	chr1:74664600-74665400	Enhancers	Hela-S3	cervix
25	chr1:74664600-74665600	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:74664600-74665600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:74664600-74665600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:74664600-74668800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:74664600-74671200	Weak transcription	Fetal Intestine Small	intestine
30	chr1:74664800-74665200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:74664800-74665400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:74664800-74665400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:74664800-74665400	Enhancers	HepG2	liver
34	chr1:74664800-74665600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:74664800-74665600	Enhancers	Fetal Brain Male	brain
36	chr1:74664800-74665600	Enhancers	Small Intestine	intestine
37	chr1:74664800-74665800	Enhancers	Liver	Liver
38	chr1:74664800-74666000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:74664800-74666000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:74664800-74666400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:74664800-74666600	Weak transcription	Placenta	Placenta
42	chr1:74664800-74667200	Enhancers	Fetal Heart	heart
43	chr1:74664800-74668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:74664800-74668200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:74664800-74668400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:74664800-74668800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:74664800-74669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:74664800-74669600	Weak transcription	Fetal Lung	lung
49	chr1:74664800-74670800	Weak transcription	Fetal Stomach	stomach
50	chr1:74664800-74672000	Weak transcription	Fetal Thymus	thymus

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