Variant report

Variant	rs12097583
Chromosome Location	chr1:153723037-153723038
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	RCOR1	chr1:153722856-153723526	K562	blood:	n/a	n/a
2	JUN	chr1:153722673-153723211	K562	blood:	n/a	chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722951-153722962 chr1:153722949-153722958 chr1:153722948-153722960 chr1:153722949-153722959
3	BHLHE40	chr1:153721885-153723522	K562	blood:	n/a	chr1:153722139-153722152
4	ZMIZ1	chr1:153722973-153723276	K562	blood:	n/a	n/a
5	JUN	chr1:153721642-153723311	K562	blood:	n/a	chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722951-153722962 chr1:153722949-153722958 chr1:153722948-153722960 chr1:153722949-153722959
6	CTCF	chr1:153723020-153723170	HPF	lung:	n/a	n/a
7	TAL1	chr1:153722833-153723522	K562	blood:	n/a	n/a
8	NR3C1	chr1:153722791-153723270	A549	lung:	n/a	chr1:153723049-153723075 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723053-153723071 chr1:153723055-153723069 chr1:153723054-153723070 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723055-153723069 chr1:153723051-153723072
9	GATA2	chr1:153722849-153723578	K562	blood:	n/a	chr1:153723035-153723044 chr1:153723337-153723346
10	TEAD4	chr1:153722789-153723554	K562	blood:	n/a	n/a
11	CTCF	chr1:153721665-153723546	A549	lung:	n/a	chr1:153722067-153722074 chr1:153722060-153722078 chr1:153722055-153722076 chr1:153722061-153722077
12	NR3C1	chr1:153722876-153723305	A549	lung:	n/a	chr1:153723049-153723075 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723053-153723071 chr1:153723055-153723069 chr1:153723054-153723070 chr1:153723054-153723070 chr1:153723049-153723075 chr1:153723055-153723069 chr1:153723051-153723072
13	EBF1	chr1:153722822-153723233	GM12878	blood:	n/a	n/a
14	RCOR1	chr1:153722789-153723595	K562	blood:	n/a	n/a
15	HDAC2	chr1:153722859-153723144	K562	blood:	n/a	n/a
16	CEBPB	chr1:153722991-153723280	K562	blood:	n/a	n/a
17	ATF1	chr1:153723031-153723445	K562	blood:	n/a	n/a
18	JUND	chr1:153722774-153723417	K562	blood:	n/a	chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722949-153722959 chr1:153722951-153722962 chr1:153722949-153722958 chr1:153722948-153722960 chr1:153722949-153722959
19	ZNF384	chr1:153722815-153723089	K562	blood:	n/a	n/a
20	EGR1	chr1:153722851-153723082	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153720991..153724810-chr1:153725795..153729552,4	K562	blood:
2	chr1:153720924..153726415-chr1:153745287..153750957,9	MCF-7	breast:
3	chr1:153650179..153650905-chr1:153722557..153723212,2	MCF-7	breast:
4	chr1:153721868..153723667-chr1:153746625..153749637,3	MCF-7	breast:
5	chr1:153698814..153704322-chr1:153719587..153724035,6	MCF-7	breast:
6	chr1:153721928..153724175-chr1:153731100..153734049,2	MCF-7	breast:

Variant related genes	Relation type
INTS3	TF binding region
ENSG00000143624	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000238511	Chromatin interaction
ENSG00000199565	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10082235	1.00[CHB][hapmap]
rs11264299	0.94[EUR][1000 genomes]
rs11264336	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1132619	0.96[EUR][1000 genomes]
rs12062022	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070179	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070559	0.94[EUR][1000 genomes]
rs12071801	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076697	0.94[EUR][1000 genomes]
rs12097043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34527123	1.00[ASN][1000 genomes]
rs36064263	0.96[EUR][1000 genomes]
rs3891075	1.00[CHB][hapmap]
rs4073768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265191	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55658698	0.94[EUR][1000 genomes]
rs55778008	0.94[EUR][1000 genomes]
rs56167936	0.96[EUR][1000 genomes]
rs56910871	0.94[EUR][1000 genomes]
rs57314764	0.83[EUR][1000 genomes]
rs60100741	0.84[EUR][1000 genomes]
rs60316596	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60827720	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803563	0.94[EUR][1000 genomes]
rs61803565	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61803566	0.88[EUR][1000 genomes]
rs61803567	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61803571	0.91[EUR][1000 genomes]
rs61803573	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61803652	1.00[ASN][1000 genomes]
rs6427085	0.90[EUR][1000 genomes]
rs6660232	0.84[EUR][1000 genomes]
rs6663011	0.94[EUR][1000 genomes]
rs6663988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6668229	0.83[EUR][1000 genomes]
rs6672371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682411	0.96[EUR][1000 genomes]
rs6687602	0.96[EUR][1000 genomes]
rs6689176	0.94[EUR][1000 genomes]
rs6692298	1.00[CHB][hapmap]
rs74115713	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512561	0.84[EUR][1000 genomes]
rs7515716	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7520045	0.84[EUR][1000 genomes]
rs7520235	0.83[EUR][1000 genomes]
rs7533987	1.00[CHB][hapmap]
rs7536700	1.00[CHB][hapmap]
rs7543790	1.00[CHB][hapmap]
rs7556155	0.92[EUR][1000 genomes]
rs7556379	0.84[EUR][1000 genomes]
rs7556575	0.83[AMR][1000 genomes];0.98[EUR][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	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
12	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
16	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
17	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12097583	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
4	chr1:153712800-153725600	Strong transcription	Fetal Lung	lung
5	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
8	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
9	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
13	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:153713000-153725600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr1:153713000-153728600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
17	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:153713000-153747000	Strong transcription	Dnd41	blood
24	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:153715400-153724600	Strong transcription	NH-A	brain
27	chr1:153715400-153724800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:153715600-153725600	Strong transcription	NHEK	skin
30	chr1:153715600-153727600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
32	chr1:153715800-153724400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:153715800-153728400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:153716400-153723200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:153716400-153723200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:153717000-153723400	Strong transcription	GM12878-XiMat	blood
38	chr1:153718400-153727800	Strong transcription	Primary B cells from cord blood	blood
39	chr1:153718800-153724400	Strong transcription	NHLF	lung
40	chr1:153718800-153730000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:153719400-153725000	Strong transcription	Fetal Brain Male	brain
42	chr1:153719400-153727800	Strong transcription	HMEC	breast
43	chr1:153719400-153729000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:153719800-153731200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:153720000-153723400	Weak transcription	Pancreas	Pancrea
47	chr1:153720000-153726800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:153720200-153723800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:153720400-153723400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:153721000-153723400	Enhancers	Left Ventricle	heart

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