Variant report

Variant	rs4839273
Chromosome Location	chr1:113502552-113502553
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	POLR2A	chr1:113502410-113503784	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:113502508-113503768	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113460690..113462402-chr1:113501543..113503150,2	K562	blood:
2	chr1:113250102..113252042-chr1:113500329..113503036,2	K562	blood:

Variant related genes	Relation type
SLC16A1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10399593	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1049434	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10776763	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857981	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10857982	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857983	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11102559	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11102562	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102565	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102568	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028967	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037621	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043035	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1344429	0.80[EUR][1000 genomes]
rs1539625	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1629027	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17030905	0.93[GIH][hapmap]
rs2002402	0.82[EUR][1000 genomes]
rs2360009	0.82[EUR][1000 genomes]
rs3789592	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3889656	0.86[CEU][hapmap]
rs4301628	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57549167	0.85[EUR][1000 genomes]
rs61819971	0.82[AMR][1000 genomes]
rs61819997	0.85[EUR][1000 genomes]
rs6537764	0.87[ASN][1000 genomes]
rs6537765	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6663872	0.93[ASN][1000 genomes]
rs6682142	0.91[EUR][1000 genomes]
rs7169	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7551223	0.92[ASN][1000 genomes]
rs7556664	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9787311	0.83[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4839273	DENND2C	cis	parietal	SCAN
rs4839273	LRIG2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113499600-113525600	Weak transcription	Spleen	Spleen
2	chr1:113499800-113514800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:113500200-113509800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:113500200-113524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:113500200-113528600	Weak transcription	Lung	lung
6	chr1:113500200-113529000	Weak transcription	Esophagus	oesophagus
7	chr1:113500400-113520200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:113500600-113507000	Weak transcription	Ovary	ovary
9	chr1:113500600-113507200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:113500600-113510000	Weak transcription	Fetal Intestine Large	intestine
11	chr1:113500600-113510200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:113500600-113515000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:113500600-113535400	Weak transcription	Aorta	Aorta
14	chr1:113500800-113502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:113500800-113503000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:113500800-113503400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:113500800-113503400	Weak transcription	Fetal Lung	lung
18	chr1:113500800-113505600	Weak transcription	Liver	Liver
19	chr1:113500800-113506200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:113500800-113507000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:113500800-113507200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:113500800-113507400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:113500800-113509600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:113500800-113509800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:113500800-113510200	Weak transcription	HSMMtube	muscle
26	chr1:113500800-113510400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:113500800-113510400	Weak transcription	NH-A	brain
28	chr1:113500800-113515400	Weak transcription	Fetal Kidney	kidney
29	chr1:113500800-113515800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:113501000-113502800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:113501000-113503000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:113501000-113503000	Weak transcription	Primary T cells from cord blood	blood
33	chr1:113501000-113503000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:113501000-113503000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:113501000-113503200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:113501000-113503200	Weak transcription	A549	lung
37	chr1:113501000-113503400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:113501000-113504000	Weak transcription	Fetal Stomach	stomach
39	chr1:113501000-113506800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:113501000-113506800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:113501000-113508600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:113501000-113508600	Weak transcription	Fetal Thymus	thymus
43	chr1:113501000-113508800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113501000-113510000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:113501000-113510000	Weak transcription	Placenta	Placenta
46	chr1:113501000-113510200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:113501000-113510800	Weak transcription	Stomach Mucosa	stomach
48	chr1:113501000-113525600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:113501200-113503000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:113501200-113503400	Weak transcription	Adipose Nuclei	Adipose

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