Variant report

Variant	rs1311620
Chromosome Location	chr4:100013091-100013092
allele	C/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	POLR2A	chr4:100012798-100013417	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr4:100012946-100013316	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100008800..100013313-chr4:100866380..100869813,5	K562	blood:

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1042364	0.84[CEU][hapmap]
rs1042365	0.84[CEU][hapmap]
rs1126672	0.84[CEU][hapmap]
rs1133485	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1154400	1.00[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1154401	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1154403	0.93[EUR][1000 genomes]
rs1154405	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1154406	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1154410	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1230155	0.88[CEU][hapmap];0.91[YRI][hapmap]
rs12502237	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12506256	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12697	0.91[YRI][hapmap]
rs13107558	0.82[EUR][1000 genomes]
rs13110176	0.84[CEU][hapmap]
rs13110764	0.84[CEU][hapmap]
rs13112176	0.84[CEU][hapmap]
rs1311615	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311616	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311617	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311618	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311619	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13129488	0.84[CEU][hapmap]
rs13133647	0.84[CEU][hapmap]
rs13138294	0.84[CEU][hapmap]
rs13143133	0.84[CEU][hapmap]
rs1377689	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13832	0.91[CEU][hapmap];0.82[YRI][hapmap]
rs1453872	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1453873	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1453874	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17217949	0.84[CEU][hapmap]
rs17218003	0.84[CEU][hapmap]
rs17218073	0.84[CEU][hapmap]
rs17218108	0.84[CEU][hapmap]
rs17218141	0.84[CEU][hapmap]
rs17218162	0.84[CEU][hapmap]
rs17218239	0.84[CEU][hapmap]
rs17218288	0.84[CEU][hapmap]
rs17218560	0.84[CEU][hapmap]
rs17218602	0.84[CEU][hapmap]
rs17817359	0.84[CEU][hapmap]
rs17817868	0.84[CEU][hapmap]
rs17817958	0.84[CEU][hapmap]
rs1840228	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1840229	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1840230	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1840231	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1901922	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1984362	0.81[CEU][hapmap]
rs1984364	0.81[CEU][hapmap]
rs2034696	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602840	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602841	0.86[EUR][1000 genomes]
rs2602845	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602846	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602847	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602851	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602853	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602854	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602855	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602856	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2602857	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2602858	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602859	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2602860	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2602862	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2602875	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602876	0.81[AMR][1000 genomes]
rs2602877	0.81[AMR][1000 genomes]
rs2602878	0.81[AMR][1000 genomes]
rs2602895	0.84[CEU][hapmap]
rs2602896	0.83[CEU][hapmap]
rs2851246	0.84[CEU][hapmap]
rs2851247	0.84[CEU][hapmap]
rs2851248	0.84[CEU][hapmap]
rs2851259	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2851263	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851265	0.83[AMR][1000 genomes]
rs2851267	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2851268	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851269	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851270	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2851274	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2851277	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851278	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851279	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2851283	0.83[AMR][1000 genomes]
rs2851284	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2851285	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2851286	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs29001203	0.84[CEU][hapmap]
rs2924580	0.80[EUR][1000 genomes]
rs2924585	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3018046	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3018047	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3018048	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3100629	0.81[AMR][1000 genomes]
rs3100630	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3133152	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34936974	0.84[CEU][hapmap]
rs4235435	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4235436	1.00[ASN][1000 genomes]
rs4699700	0.92[YRI][hapmap]
rs4699712	0.84[CEU][hapmap]
rs4699713	0.84[CEU][hapmap]
rs4699714	0.84[CEU][hapmap]
rs4699717	0.80[CEU][hapmap]
rs6822830	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6831225	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6831257	0.87[AFR][1000 genomes]
rs7434491	0.81[CEU][hapmap]
rs7669636	0.84[CEU][hapmap]
rs7669660	0.91[YRI][hapmap]
rs7670060	0.84[CEU][hapmap]
rs7670241	0.84[CEU][hapmap]
rs7683704	0.91[YRI][hapmap]
rs7689753	0.86[CEU][hapmap]
rs7694646	0.84[CEU][hapmap]
rs896992	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs9761048	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS 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	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1849572	chr4:100007243-100024396	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1311620	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100007800-100013400	Active TSS	K562	blood
2	chr4:100011200-100013600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:100011400-100013600	Enhancers	Colon Smooth Muscle	Colon
4	chr4:100011400-100025800	Weak transcription	Esophagus	oesophagus
5	chr4:100011600-100025600	Weak transcription	Primary T cells from cord blood	blood
6	chr4:100011800-100020600	Weak transcription	Fetal Intestine Small	intestine
7	chr4:100012000-100013200	Enhancers	Rectal Smooth Muscle	rectum
8	chr4:100012200-100013200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr4:100012200-100014400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:100012200-100015000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:100012400-100013800	Enhancers	Small Intestine	intestine
12	chr4:100012600-100013400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:100012800-100013200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:100012800-100013200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:100012800-100013200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:100012800-100013200	Active TSS	HMEC	breast
17	chr4:100012800-100013600	Weak transcription	Adipose Nuclei	Adipose
18	chr4:100012800-100014000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:100012800-100014400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
21	chr4:100013000-100013200	Flanking Active TSS	NHEK	skin
22	chr4:100013000-100013400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:100013000-100013400	Weak transcription	HepG2	liver
24	chr4:100013000-100013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:100013000-100014800	Weak transcription	Fetal Lung	lung
26	chr4:100013000-100020200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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