Variant report

Variant	rs2149036
Chromosome Location	chr1:113479886-113479887
allele	A/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	POLR2A	chr1:113479506-113480264	U87	brain:	n/a	n/a
2	MXI1	chr1:113479761-113480367	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:113479633-113480227	U87	brain:	n/a	n/a
4	ZMIZ1	chr1:113479787-113479906	K562	blood:	n/a	n/a
5	ZNF384	chr1:113479812-113479966	K562	blood:	n/a	n/a
6	RUNX3	chr1:113479833-113480206	GM12878	blood:	n/a	n/a
7	BCL11A	chr1:113479750-113479936	GM12878	blood:	n/a	n/a
8	STAT3	chr1:113479747-113480009	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr1:113479751-113480368	MCF10A-Er-Src	breast:	n/a	n/a
10	BATF	chr1:113479742-113479990	GM12878	blood:	n/a	n/a
11	FOS	chr1:113479708-113480031	MCF10A-Er-Src	breast:	n/a	chr1:113480005-113480014
12	BHLHE40	chr1:113479780-113480052	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:113479546-113480498	SK-N-MC	brain:	n/a	n/a
14	JUN	chr1:113477995-113481391	K562	blood:	n/a	chr1:113478380-113478388 chr1:113480192-113480201 chr1:113478380-113478387 chr1:113478380-113478388 chr1:113480005-113480014 chr1:113478379-113478389 chr1:113478672-113478685 chr1:113478651-113478664
15	STAT3	chr1:113479737-113480008	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr1:113479691-113480058	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr1:113479738-113480022	MCF10A-Er-Src	breast:	n/a	chr1:113480005-113480014
18	FOS	chr1:113479694-113480058	MCF10A-Er-Src	breast:	n/a	chr1:113480005-113480014
19	FOS	chr1:113479487-113480095	MCF10A-Er-Src	breast:	n/a	chr1:113480005-113480014
20	POLR2A	chr1:113479633-113480199	U87	brain:	n/a	n/a
21	MYC	chr1:113479656-113479908	MCF10A-Er-Src	breast:	n/a	n/a
22	MAZ	chr1:113479851-113480109	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr1:113479846-113480105	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113476476..113482692-chr1:113494893..113501777,18	K562	blood:
2	chr1:113479847..113481984-chr1:113483507..113487359,6	K562	blood:

Variant related genes	Relation type
SLC16A1	TF binding region
ENSG00000226419	Chromatin interaction
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11102560	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12064292	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126192	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216537	0.81[CEU][hapmap]
rs17440299	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493313	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494145	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17494180	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1936311	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28556822	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849174	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838971	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839270	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839272	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4839276	0.82[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55768060	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55982206	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55992320	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56007797	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019044	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56220197	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676446	0.90[EUR][1000 genomes]
rs6676864	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66899043	0.95[EUR][1000 genomes]
rs72683432	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683434	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683453	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72683454	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72683459	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72683463	0.90[AMR][1000 genomes]
rs72683468	0.84[AMR][1000 genomes]
rs7518984	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524567	0.95[EUR][1000 genomes]
rs7536532	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540321	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7542229	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545602	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548109	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550843	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7552903	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9429505	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429709	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429710	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer 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	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2149036	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113458000-113490600	Weak transcription	Right Atrium	heart
2	chr1:113460400-113481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:113460800-113480200	Weak transcription	Adipose Nuclei	Adipose
4	chr1:113460800-113480600	Weak transcription	Ovary	ovary
5	chr1:113466400-113496400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:113467000-113480200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:113467000-113480200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:113467000-113480200	Weak transcription	Thymus	Thymus
9	chr1:113467000-113482000	Weak transcription	Aorta	Aorta
10	chr1:113467000-113482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:113467000-113493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:113467000-113495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:113467000-113497400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:113467200-113496400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:113468000-113496200	Weak transcription	Fetal Brain Female	brain
16	chr1:113468200-113495400	Weak transcription	Psoas Muscle	Psoas
17	chr1:113469800-113480600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:113469800-113495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:113469800-113495600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:113469800-113497000	Weak transcription	Fetal Stomach	stomach
21	chr1:113470800-113480600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:113471800-113480200	Weak transcription	GM12878-XiMat	blood
23	chr1:113471800-113493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:113472000-113484000	Weak transcription	Left Ventricle	heart
25	chr1:113472600-113480600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:113472800-113480200	Weak transcription	Right Ventricle	heart
27	chr1:113473000-113480200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:113473000-113495000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:113473000-113495400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:113474800-113480000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:113475400-113481200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:113476600-113481600	Enhancers	Hela-S3	cervix
33	chr1:113476800-113481000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:113476800-113481200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:113477000-113481200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:113477000-113481400	Enhancers	HMEC	breast
37	chr1:113477400-113480600	Enhancers	HSMM	muscle
38	chr1:113477400-113481200	Enhancers	HUVEC	blood vessel
39	chr1:113477400-113481400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:113477400-113481400	Enhancers	Osteobl	bone
41	chr1:113477600-113480000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:113477600-113480400	Weak transcription	Stomach Mucosa	stomach
43	chr1:113478000-113481000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr1:113478000-113481200	Enhancers	HepG2	liver
45	chr1:113478000-113481400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
46	chr1:113478200-113481200	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:113478400-113481200	Enhancers	Liver	Liver
48	chr1:113478400-113481400	Enhancers	Rectal Smooth Muscle	rectum
49	chr1:113478400-113483400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:113478600-113480600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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