Variant report

Variant	rs4839270
Chromosome Location	chr1:113477320-113477321
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113476476..113482692-chr1:113494893..113501777,18	K562	blood:
2	chr1:113476800..113479671-chr1:113497569..113500244,3	MCF-7	breast:
3	chr1:113475729..113477764-chr1:113481797..113484434,3	K562	blood:

Variant related genes	Relation type
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]
rs2149036	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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
rs4839270	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113458000-113490600	Weak transcription	Right Atrium	heart
2	chr1:113458600-113478400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:113460400-113479800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:113460400-113481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:113460600-113478400	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:113460800-113480200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:113460800-113480600	Weak transcription	Ovary	ovary
8	chr1:113461200-113478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:113464800-113477800	Weak transcription	NH-A	brain
10	chr1:113466400-113496400	Weak transcription	Primary T cells from cord blood	blood
11	chr1:113466800-113479800	Weak transcription	Fetal Lung	lung
12	chr1:113467000-113478000	Weak transcription	NHLF	lung
13	chr1:113467000-113478400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:113467000-113479600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:113467000-113480200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:113467000-113480200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:113467000-113480200	Weak transcription	Thymus	Thymus
18	chr1:113467000-113482000	Weak transcription	Aorta	Aorta
19	chr1:113467000-113482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:113467000-113493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:113467000-113495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:113467000-113497400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:113467200-113496400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:113467400-113477400	Weak transcription	A549	lung
25	chr1:113467800-113477400	Weak transcription	Osteobl	bone
26	chr1:113468000-113496200	Weak transcription	Fetal Brain Female	brain
27	chr1:113468200-113495400	Weak transcription	Psoas Muscle	Psoas
28	chr1:113468400-113478600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:113469400-113478200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:113469800-113480600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:113469800-113495600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:113469800-113495600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:113469800-113497000	Weak transcription	Fetal Stomach	stomach
34	chr1:113470800-113480600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:113471000-113478400	Weak transcription	Liver	Liver
36	chr1:113471000-113479600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:113471200-113477400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:113471200-113478000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:113471200-113478400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:113471400-113477400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:113471800-113477400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:113471800-113480200	Weak transcription	GM12878-XiMat	blood
43	chr1:113471800-113493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113472000-113477400	Weak transcription	HUVEC	blood vessel
45	chr1:113472000-113477800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:113472000-113478200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:113472000-113478400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:113472000-113479800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:113472000-113484000	Weak transcription	Left Ventricle	heart
50	chr1:113472600-113479400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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