Variant report

Variant	rs16830728
Chromosome Location	chr2:152981335-152981336
allele	G/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	MAFK	chr2:152981134-152981375	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
STAM2	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10182220	0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs10497094	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497096	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11883513	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11883564	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11883823	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11895924	0.81[CHD][hapmap];0.82[GIH][hapmap]
rs11901219	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614451	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12615121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995179	0.87[AMR][1000 genomes]
rs13003831	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13008702	1.00[CEU][hapmap]
rs13015485	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13017394	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830726	0.89[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs16830744	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830853	1.00[CEU][hapmap]
rs34462050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820706	0.89[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs4664083	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59342964	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67622277	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72621654	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1004308	chr2:152980087-153154534	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv535985	chr2:152980087-153154534	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Adverse response to chemotherapy in breast cancer (alopecia)	24025145	GWAS catalog

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152968000-152995800	Weak transcription	HSMMtube	muscle
2	chr2:152969400-152989000	Weak transcription	HepG2	liver
3	chr2:152970000-152990800	Weak transcription	Stomach Mucosa	stomach
4	chr2:152970200-153003000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:152970800-152981400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:152971200-153008400	Weak transcription	Esophagus	oesophagus
7	chr2:152971400-153002200	Weak transcription	Brain Anterior Caudate	brain
8	chr2:152972800-152991000	Weak transcription	Gastric	stomach
9	chr2:152974200-153001400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:152974200-153017000	Weak transcription	Colonic Mucosa	Colon
11	chr2:152974800-153002000	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:152974800-153003800	Weak transcription	NHEK	skin
13	chr2:152974800-153008200	Weak transcription	Fetal Brain Female	brain
14	chr2:152975000-152987800	Weak transcription	Right Ventricle	heart
15	chr2:152975000-153003200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:152975000-153003600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:152975000-153005400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:152975200-152990000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:152975400-152982400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:152975400-152988800	Weak transcription	A549	lung
21	chr2:152975600-152982400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:152975600-152982600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:152975600-152986600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:152975800-152982200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:152975800-152982400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:152975800-152982400	Strong transcription	Liver	Liver
27	chr2:152975800-152982400	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:152975800-152982800	Strong transcription	Placenta	Placenta
29	chr2:152975800-152983800	Strong transcription	Primary T cells from cord blood	blood
30	chr2:152976000-152982200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:152976000-152982400	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:152976000-152982600	Strong transcription	Adipose Nuclei	Adipose
33	chr2:152976000-152986600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:152976000-153014800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:152976200-153010200	Weak transcription	Fetal Brain Male	brain
36	chr2:152976200-153013400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:152976400-152982200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:152976400-152983200	Weak transcription	Psoas Muscle	Psoas
39	chr2:152976400-152991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:152976400-153005000	Weak transcription	Fetal Heart	heart
41	chr2:152976400-153013400	Weak transcription	Brain Angular Gyrus	brain
42	chr2:152976600-152982200	Strong transcription	Left Ventricle	heart
43	chr2:152976600-152982400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:152976600-152983400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:152976600-152991000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:152976600-152991200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:152976600-152991400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr2:152976800-152982400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:152976800-152991000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:152976800-152991200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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