Variant report

Variant	rs4839277
Chromosome Location	chr1:113564372-113564373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113495044..113497639-chr1:113562401..113565157,2	K562	blood:
2	chr1:113564257..113567522-chr1:113568390..113572555,4	K562	blood:
3	chr1:113496138..113497721-chr1:113563292..113564960,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1216774	1.00[ASN][1000 genomes]
rs1216776	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1216778	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17494145	0.90[EUR][1000 genomes]
rs17494180	0.91[EUR][1000 genomes]
rs4839276	0.83[EUR][1000 genomes]
rs55768060	0.87[EUR][1000 genomes]
rs55982206	0.82[EUR][1000 genomes]
rs56019044	0.83[EUR][1000 genomes]
rs6669006	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72683459	0.83[EUR][1000 genomes]
rs72683463	0.93[EUR][1000 genomes]
rs72683468	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	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
rs4839277	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113535800-113568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
3	chr1:113543200-113574400	Weak transcription	HSMM	muscle
4	chr1:113551200-113564400	Weak transcription	Adipose Nuclei	Adipose
5	chr1:113551200-113569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:113551200-113569800	Weak transcription	Left Ventricle	heart
7	chr1:113552800-113570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:113553000-113572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:113555600-113572200	Weak transcription	Primary T cells from cord blood	blood
10	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:113562400-113574000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:113563400-113564600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:113563400-113564800	Enhancers	Stomach Mucosa	stomach
14	chr1:113563800-113564800	Enhancers	Fetal Heart	heart
15	chr1:113564000-113564400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr1:113564000-113564400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:113564000-113564400	Enhancers	Colon Smooth Muscle	Colon
18	chr1:113564000-113564600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:113564000-113564600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:113564000-113564600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:113564000-113564600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:113564000-113564600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:113564000-113564600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:113564000-113564600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:113564000-113564600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:113564000-113564600	Enhancers	Rectal Smooth Muscle	rectum
27	chr1:113564000-113564600	Flanking Active TSS	HepG2	liver
28	chr1:113564000-113564800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:113564000-113564800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113564000-113564800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:113564000-113564800	Enhancers	K562	blood
32	chr1:113564000-113565000	Enhancers	Liver	Liver
33	chr1:113564000-113569600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:113564200-113564400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:113564200-113564400	Flanking Active TSS	NHEK	skin
36	chr1:113564200-113564600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:113564200-113564600	Enhancers	H1 Cell Line	embryonic stem cell
38	chr1:113564200-113564600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:113564200-113564600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:113564200-113564600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr1:113564200-113564600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:113564200-113564600	Enhancers	Fetal Intestine Large	intestine
43	chr1:113564200-113564600	Enhancers	Fetal Intestine Small	intestine
44	chr1:113564200-113564600	Enhancers	Placenta	Placenta
45	chr1:113564200-113564600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:113564200-113564600	Enhancers	A549	lung
47	chr1:113564200-113564600	Flanking Active TSS	HMEC	breast
48	chr1:113564200-113564800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:113564200-113564800	Enhancers	Brain Germinal Matrix	brain
50	chr1:113564200-113564800	Enhancers	Osteobl	bone

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