Variant report

Variant	rs12753370
Chromosome Location	chr1:74666729-74666730
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	CUX1	chr1:74666699-74666877	K562	blood:	n/a	n/a
2	CEBPB	chr1:74666607-74666817	HepG2	liver:	n/a	chr1:74666714-74666723 chr1:74666712-74666723

Variant related genes	Relation type
LRRIQ3	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10047208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs1032084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10749829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs10890102	0.92[ASN][1000 genomes]
rs10890106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs10890107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10890114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs11210402	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11210406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11210414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11210415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11210429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs12742029	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1333032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs1340472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1483782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1483785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs1483786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1483788	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17094802	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs1934729	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1984228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35254383	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4649995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4650246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4650248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs471496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505634	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518769	1.00[ASN][1000 genomes]
rs525358	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532396	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55793584	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs573721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575961	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs6424575	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658083	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6661309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6669321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6672037	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71655424	1.00[ASN][1000 genomes]
rs7524306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7535276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7538410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs7542912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792323	1.00[ASN][1000 genomes]
rs9425024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs982792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]

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

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74664200-74667400	Weak transcription	Left Ventricle	heart
2	chr1:74664200-74672000	Weak transcription	Lung	lung
3	chr1:74664200-74672000	Weak transcription	Spleen	Spleen
4	chr1:74664200-74675200	Weak transcription	Pancreas	Pancrea
5	chr1:74664600-74668800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:74664600-74671200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:74664800-74667200	Enhancers	Fetal Heart	heart
8	chr1:74664800-74668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:74664800-74668200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:74664800-74668400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:74664800-74668800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:74664800-74669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:74664800-74669600	Weak transcription	Fetal Lung	lung
14	chr1:74664800-74670800	Weak transcription	Fetal Stomach	stomach
15	chr1:74664800-74672000	Weak transcription	Fetal Thymus	thymus
16	chr1:74664800-74673600	Weak transcription	NH-A	brain
17	chr1:74664800-74674000	Weak transcription	Fetal Kidney	kidney
18	chr1:74664800-74674600	Weak transcription	HSMMtube	muscle
19	chr1:74664800-74676000	Weak transcription	HSMM	muscle
20	chr1:74664800-74680400	Weak transcription	Fetal Brain Female	brain
21	chr1:74664800-74688200	Weak transcription	Psoas Muscle	Psoas
22	chr1:74665000-74667000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:74665000-74667200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:74665000-74667400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:74665000-74667400	Weak transcription	Fetal Intestine Large	intestine
26	chr1:74665000-74668400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:74665000-74668800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:74665000-74669000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:74665000-74670000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:74665000-74670200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:74665000-74670200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:74665000-74670200	Weak transcription	NHLF	lung
33	chr1:74665000-74670400	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:74665000-74670400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:74665000-74671000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:74665000-74671000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:74665000-74671600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:74665000-74672000	Weak transcription	HMEC	breast
39	chr1:74665000-74672200	Weak transcription	Colonic Mucosa	Colon
40	chr1:74665000-74672200	Weak transcription	HUVEC	blood vessel
41	chr1:74665000-74672600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:74665000-74673000	Weak transcription	Aorta	Aorta
43	chr1:74665000-74675000	Weak transcription	Osteobl	bone
44	chr1:74665000-74675600	Weak transcription	A549	lung
45	chr1:74665000-74677000	Weak transcription	Right Ventricle	heart
46	chr1:74665000-74690200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:74665200-74666800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:74665200-74667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:74665200-74668400	Weak transcription	NHEK	skin
50	chr1:74665200-74672600	Weak transcription	Brain Germinal Matrix	brain

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