Variant report

Variant	rs4839276
Chromosome Location	chr1:113524639-113524640
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113498539..113500534-chr1:113523164..113526925,5	K562	blood:
2	chr1:113514230..113516551-chr1:113524228..113525936,2	K562	blood:

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction
ENSG00000226419	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11102560	0.83[EUR][1000 genomes]
rs12064292	0.88[EUR][1000 genomes]
rs12126192	0.83[EUR][1000 genomes]
rs1216778	0.87[EUR][1000 genomes]
rs17440299	0.81[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17493313	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs17494145	0.91[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494180	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936311	0.85[EUR][1000 genomes]
rs2149036	0.82[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28556822	0.88[EUR][1000 genomes]
rs3849174	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs4838971	0.88[EUR][1000 genomes]
rs4839270	0.82[CEU][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4839272	0.81[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839277	0.83[EUR][1000 genomes]
rs55768060	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55982206	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55992320	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007797	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56019044	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56220197	0.85[EUR][1000 genomes]
rs6669006	0.88[EUR][1000 genomes]
rs6676446	0.81[EUR][1000 genomes]
rs6676864	0.82[EUR][1000 genomes]
rs66899043	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683432	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72683434	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72683442	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72683453	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683454	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683459	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683463	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683468	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7518984	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7524567	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536532	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7540321	0.80[EUR][1000 genomes]
rs7542229	0.89[EUR][1000 genomes]
rs7545602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7548109	0.80[EUR][1000 genomes]
rs7550843	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7552903	0.81[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429505	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs9429709	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs9429710	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	esv1827123	chr1:113496841-113531848	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4839276	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113499600-113525600	Weak transcription	Spleen	Spleen
2	chr1:113500200-113528600	Weak transcription	Lung	lung
3	chr1:113500200-113529000	Weak transcription	Esophagus	oesophagus
4	chr1:113500600-113535400	Weak transcription	Aorta	Aorta
5	chr1:113501000-113525600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:113503600-113525400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:113510600-113537000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:113510800-113541800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:113511000-113525200	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:113511000-113525600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:113511000-113528600	Weak transcription	Right Ventricle	heart
12	chr1:113511000-113531200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:113511200-113525400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:113511200-113525400	Weak transcription	Psoas Muscle	Psoas
15	chr1:113511200-113525600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:113511200-113525600	Weak transcription	Fetal Lung	lung
17	chr1:113511200-113525800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:113511200-113525800	Weak transcription	Primary T cells from cord blood	blood
19	chr1:113511200-113528000	Weak transcription	NHEK	skin
20	chr1:113511200-113530000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:113511200-113538400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:113511200-113540000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:113511200-113540800	Weak transcription	HSMM	muscle
24	chr1:113511200-113545800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:113511200-113546400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:113511200-113558000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:113511200-113558600	Weak transcription	NHDF-Ad	bronchial
28	chr1:113511200-113564000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:113511400-113525400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr1:113511400-113526000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:113511800-113534000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:113511800-113540200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:113512200-113534000	Weak transcription	Fetal Stomach	stomach
34	chr1:113513600-113528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:113513600-113530800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:113513800-113525600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:113513800-113525600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:113513800-113525600	Weak transcription	GM12878-XiMat	blood
39	chr1:113513800-113528400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:113513800-113536600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:113513800-113536800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:113513800-113541000	Weak transcription	Hela-S3	cervix
43	chr1:113514000-113541200	Weak transcription	K562	blood
44	chr1:113516800-113541000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:113517000-113525400	Weak transcription	Left Ventricle	heart
46	chr1:113517000-113528600	Weak transcription	Right Atrium	heart
47	chr1:113517200-113540400	Weak transcription	HepG2	liver
48	chr1:113517400-113525600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:113517800-113542800	Weak transcription	Dnd41	blood
50	chr1:113519600-113538600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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