Variant report

Variant	rs12408349
Chromosome Location	chr1:179262334-179262335
allele	A/C
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	TAF1	chr1:179262329-179263179	PFSK-1	brain:	n/a	n/a
2	SIN3AK20	chr1:179262283-179263621	MCF-7	breast:	n/a	n/a
3	MAX	chr1:179262290-179263557	A549	lung:	n/a	chr1:179262899-179262909
4	CBX3	chr1:179262230-179263508	K562	blood:	n/a	n/a
5	MAX	chr1:179262201-179263519	MCF-7	breast:	n/a	chr1:179262899-179262909
6	TEAD4	chr1:179262262-179262922	K562	blood:	n/a	n/a
7	NFIC	chr1:179262302-179263071	SK-N-SH	brain:	n/a	chr1:179262745-179262761 chr1:179262745-179262762
8	NFIC	chr1:179262242-179263403	SK-N-SH	brain:	n/a	chr1:179262745-179262761 chr1:179262745-179262762
9	RFX5	chr1:179262312-179264773	Hela-S3	cervix:	n/a	chr1:179262827-179262836 chr1:179262822-179262838 chr1:179262752-179262769 chr1:179262754-179262763 chr1:179262823-179262837
10	NFIC	chr1:179262296-179263157	ECC-1	luminal epithelium:	n/a	chr1:179262745-179262761 chr1:179262745-179262762
11	TBL1XR1	chr1:179262332-179263086	K562	blood:	n/a	n/a
12	MAX	chr1:179262246-179263608	A549	lung:	n/a	chr1:179262899-179262909
13	RFX5	chr1:179262202-179263726	SK-N-SH	brain:	n/a	chr1:179262827-179262836 chr1:179262822-179262838 chr1:179262752-179262769 chr1:179262754-179262763 chr1:179262823-179262837
14	GATA2	chr1:179262325-179262774	K562	blood:	n/a	chr1:179262475-179262484 chr1:179262389-179262405 chr1:179262475-179262485 chr1:179262393-179262400
15	GATA2	chr1:179261437-179263120	SH-SY5Y	brain:	n/a	chr1:179262475-179262484 chr1:179262389-179262405 chr1:179262475-179262485 chr1:179262393-179262400
16	REST	chr1:179262178-179263412	H1-neurons	neurons:	n/a	chr1:179262965-179262978 chr1:179263116-179263129
17	UBTF	chr1:179262326-179263416	K562	blood:	n/a	n/a
18	MAX	chr1:179262331-179263453	HepG2	liver:	n/a	chr1:179262899-179262909
19	RCOR1	chr1:179262311-179263455	K562	blood:	n/a	n/a
20	MXI1	chr1:179262213-179263720	SK-N-SH	brain:	n/a	n/a
21	GATA1	chr1:179261456-179263358	PBDE	blood:	n/a	chr1:179262475-179262484 chr1:179262389-179262405 chr1:179262475-179262485 chr1:179262393-179262400
22	RCOR1	chr1:179262318-179263228	K562	blood:	n/a	n/a
23	TEAD4	chr1:179262241-179263502	K562	blood:	n/a	n/a
24	PML	chr1:179262235-179263303	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
2	chr1:179260929..179262434-chr1:179560041..179562229,2	MCF-7	breast:
3	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
4	chr1:179050855..179052664-chr1:179261724..179264711,2	K562	blood:
5	chr1:179261306..179262860-chr1:179282015..179283875,2	K562	blood:

Variant related genes	Relation type
SOAT1	TF binding region
ENSG00000263633	Chromatin interaction
ENSG00000162782	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000162779	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1046385	1.00[ASW][hapmap]
rs10494520	1.00[CHB][hapmap]
rs10798665	0.88[CHB][hapmap]
rs10798670	1.00[CHB][hapmap]
rs10913733	1.00[CHB][hapmap]
rs12022539	1.00[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs12026030	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028643	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12035050	0.90[EUR][1000 genomes]
rs12039884	0.90[EUR][1000 genomes]
rs12045521	0.90[EUR][1000 genomes]
rs12049122	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12049237	1.00[CEU][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes]
rs12073970	1.00[CHB][hapmap]
rs12097041	1.00[CHB][hapmap]
rs12120123	1.00[CHB][hapmap]
rs12130876	1.00[CHB][hapmap]
rs12131473	1.00[CHB][hapmap]
rs12131475	1.00[CHB][hapmap]
rs12134114	1.00[CHB][hapmap]
rs12138436	1.00[CHB][hapmap]
rs12138619	1.00[CHB][hapmap]
rs12402165	1.00[CEU][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes]
rs12404921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405133	1.00[CHB][hapmap]
rs12405321	1.00[CHB][hapmap]
rs12408668	0.91[EUR][1000 genomes]
rs12725126	1.00[CHB][hapmap]
rs12740455	1.00[CHB][hapmap]
rs12745772	1.00[CHB][hapmap]
rs12759446	1.00[CHB][hapmap]
rs1325194	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap]
rs13306731	1.00[CHB][hapmap]
rs13374852	1.00[CHB][hapmap]
rs1475798	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.97[EUR][1000 genomes]
rs16853917	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes]
rs16853936	1.00[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs16854009	0.94[CHB][hapmap]
rs17362081	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[AFR][1000 genomes]
rs2068234	0.83[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2152317	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2636266	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2636278	0.81[CHB][hapmap]
rs2636289	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2636290	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[AFR][1000 genomes]
rs2793791	1.00[AFR][1000 genomes]
rs2793804	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2793805	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2793807	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2793808	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2816179	0.94[EUR][1000 genomes]
rs2816180	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3122378	0.84[ASN][1000 genomes]
rs3753524	1.00[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs380951	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818433	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap]
rs4077551	1.00[CHB][hapmap]
rs4077552	1.00[CHB][hapmap]
rs410589	0.84[ASN][1000 genomes]
rs4133136	1.00[CHB][hapmap]
rs413881	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425858	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4478776	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4651014	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs58284152	0.91[EUR][1000 genomes]
rs58948941	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59777301	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60595009	0.91[EUR][1000 genomes]
rs61821690	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61821735	0.99[EUR][1000 genomes]
rs61821737	0.96[EUR][1000 genomes]
rs61821738	0.96[EUR][1000 genomes]
rs61821739	0.97[EUR][1000 genomes]
rs61821740	0.97[EUR][1000 genomes]
rs61824363	0.97[EUR][1000 genomes]
rs61824364	0.97[EUR][1000 genomes]
rs61824365	0.95[EUR][1000 genomes]
rs61824368	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61824371	0.90[EUR][1000 genomes]
rs61824388	0.90[EUR][1000 genomes]
rs61824389	0.90[EUR][1000 genomes]
rs6669967	1.00[CHB][hapmap]
rs6675772	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694339	0.91[EUR][1000 genomes]
rs7414502	0.97[EUR][1000 genomes]
rs7547733	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs931441	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12408349	ABL2	cis	cerebellum	SCAN
rs12408349	LHX4	cis	parietal	SCAN
rs12408349	ABL2	cis	parietal	SCAN
rs12408349	FAM20B	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179258400-179262400	Weak transcription	Fetal Kidney	kidney
2	chr1:179258600-179262400	Weak transcription	Pancreas	Pancrea
3	chr1:179258600-179262400	Weak transcription	Stomach Mucosa	stomach
4	chr1:179258600-179262600	Weak transcription	Gastric	stomach
5	chr1:179258600-179262600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:179258800-179262400	Weak transcription	Colonic Mucosa	Colon
7	chr1:179260800-179262400	Enhancers	Brain Hippocampus Middle	brain
8	chr1:179261400-179262400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:179261400-179262400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:179261400-179262400	Enhancers	Brain Angular Gyrus	brain
11	chr1:179261400-179262400	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:179261600-179262400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:179261600-179262400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:179261600-179262400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:179261600-179262400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:179261600-179262400	Enhancers	Brain Substantia Nigra	brain
17	chr1:179261600-179262400	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr1:179261800-179262400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:179261800-179262800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:179261800-179265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:179262000-179262400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:179262000-179262400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:179262000-179262400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:179262000-179262400	Enhancers	Brain Cingulate Gyrus	brain
25	chr1:179262000-179262400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:179262000-179262400	Enhancers	Fetal Brain Male	brain
27	chr1:179262000-179262400	Enhancers	Placenta	Placenta
28	chr1:179262000-179262800	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr1:179262000-179264200	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:179262200-179262400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:179262200-179262400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:179262200-179262400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:179262200-179262400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:179262200-179262400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:179262200-179262400	Enhancers	Primary B cells from cord blood	blood
36	chr1:179262200-179262400	Enhancers	Primary B cells from peripheral blood	blood
37	chr1:179262200-179262400	Enhancers	Primary T cells from cord blood	blood
38	chr1:179262200-179262400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:179262200-179262400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr1:179262200-179262400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:179262200-179262400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:179262200-179262400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:179262200-179262400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:179262200-179262400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr1:179262200-179262400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:179262200-179262400	Enhancers	Adipose Nuclei	Adipose
47	chr1:179262200-179262400	Enhancers	Fetal Heart	heart
48	chr1:179262200-179262400	Enhancers	Fetal Intestine Large	intestine
49	chr1:179262200-179262400	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr1:179262200-179262400	Enhancers	Fetal Muscle Trunk	muscle

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