Variant report

Variant	rs4515601
Chromosome Location	chr8:89337704-89337705
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	SIN3A	chr8:89337488-89337852	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr8:89337526-89337771	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr8:89337537-89337737	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr8:89337619-89337726	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr8:89336029-89341963	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:89336276..89338217-chr8:89340889..89343054,2	K562	blood:
2	chr8:89335175..89338098-chr8:89338927..89340871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253553	TF binding region
ENSG00000253553	Chromatin interaction
ENSG00000156103	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10088444	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10283316	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10481112	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10504845	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1094206	0.85[ASN][1000 genomes]
rs10955586	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12155798	0.82[ASN][1000 genomes]
rs12156301	0.87[ASN][1000 genomes]
rs12548636	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12682164	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13251103	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1386767	0.82[ASN][1000 genomes]
rs1394514	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1394517	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1394518	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1394519	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1463923	0.97[ASN][1000 genomes]
rs1504804	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs1601818	0.81[ASN][1000 genomes]
rs1601819	0.82[ASN][1000 genomes]
rs1601820	0.82[ASN][1000 genomes]
rs1601821	0.82[ASN][1000 genomes]
rs1617649	0.82[ASN][1000 genomes]
rs1685541	0.85[ASN][1000 genomes]
rs1685549	0.82[ASN][1000 genomes]
rs1685551	0.82[ASN][1000 genomes]
rs1685553	0.82[ASN][1000 genomes]
rs1685554	0.82[ASN][1000 genomes]
rs1685559	0.82[ASN][1000 genomes]
rs16881203	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs16882450	0.85[ASN][1000 genomes]
rs16892543	0.80[ASN][1000 genomes]
rs1700150	0.82[ASN][1000 genomes]
rs1700154	0.81[ASN][1000 genomes]
rs1700155	0.82[ASN][1000 genomes]
rs1857753	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857754	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857755	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875904	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134962	0.85[ASN][1000 genomes]
rs2134964	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2656311	0.85[ASN][1000 genomes]
rs2656312	0.82[ASN][1000 genomes]
rs28417952	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28705947	0.80[EUR][1000 genomes]
rs3105405	0.85[ASN][1000 genomes]
rs3105406	0.85[ASN][1000 genomes]
rs3105407	0.85[ASN][1000 genomes]
rs3105409	0.85[ASN][1000 genomes]
rs3110414	0.85[ASN][1000 genomes]
rs3110415	0.85[ASN][1000 genomes]
rs3110416	0.85[ASN][1000 genomes]
rs3110417	0.83[ASN][1000 genomes]
rs35889496	0.80[EUR][1000 genomes]
rs4246109	0.80[ASN][1000 genomes]
rs4246111	0.90[JPT][hapmap]
rs4246112	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4246113	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4246115	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4275260	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4305946	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4320597	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4395936	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434662	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4463475	0.82[EUR][1000 genomes]
rs4483202	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4548227	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625076	0.82[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4961086	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961087	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961089	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961090	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961093	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4961094	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4961096	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56084092	0.85[ASN][1000 genomes]
rs56187488	0.97[ASN][1000 genomes]
rs6989866	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7009149	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014590	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7828497	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7835845	0.88[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838159	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821100	0.82[ASN][1000 genomes]
rs821111	0.85[ASN][1000 genomes]
rs821114	0.85[ASN][1000 genomes]
rs821117	0.82[ASN][1000 genomes]
rs821118	0.81[ASN][1000 genomes]
rs821119	0.82[ASN][1000 genomes]
rs821120	0.85[ASN][1000 genomes]
rs821121	0.85[ASN][1000 genomes]
rs866592	0.82[ASN][1000 genomes]
rs9656892	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831386	chr8:89209788-89403546	Enhancers Genic enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4515601	MMP16	cis	lung	GTEx
rs4515601	MMP16	cis	Adipose Subcutaneous	GTEx
rs4515601	MMP16	cis	Skin Sun Exposed Lower leg	GTEx
rs4515601	MMP16	cis	Thyroid	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89326600-89338200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:89333200-89341600	Active TSS	Fetal Brain Female	brain
3	chr8:89334600-89341600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:89335000-89341400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr8:89335000-89341400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:89335200-89341200	Active TSS	Brain Germinal Matrix	brain
7	chr8:89335800-89337800	Flanking Active TSS	Osteobl	bone
8	chr8:89335800-89339000	Active TSS	Fetal Muscle Leg	muscle
9	chr8:89335800-89341200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr8:89336000-89337800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:89336000-89340200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr8:89336000-89340800	Active TSS	Stomach Smooth Muscle	stomach
13	chr8:89336000-89341000	Active TSS	Aorta	Aorta
14	chr8:89336000-89341000	Active TSS	Fetal Stomach	stomach
15	chr8:89336000-89341400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr8:89336000-89341400	Active TSS	Brain Angular Gyrus	brain
17	chr8:89336200-89338000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr8:89336200-89338600	Active TSS	Brain Hippocampus Middle	brain
19	chr8:89336200-89338600	Flanking Active TSS	HUVEC	blood vessel
20	chr8:89336200-89341400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr8:89336200-89341400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr8:89336200-89341400	Active TSS	Brain Anterior Caudate	brain
23	chr8:89336400-89338000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:89336400-89338000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr8:89336400-89338000	Enhancers	Fetal Heart	heart
26	chr8:89336400-89338400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr8:89336400-89340800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr8:89336400-89341000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:89336400-89341200	Active TSS	Brain Cingulate Gyrus	brain
30	chr8:89336600-89337800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr8:89336600-89340400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr8:89336800-89338000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr8:89336800-89338400	Weak transcription	Colon Smooth Muscle	Colon
34	chr8:89336800-89341200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr8:89337000-89338200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr8:89337000-89341200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:89337000-89341400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:89337200-89337800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr8:89337200-89341200	Active TSS	Fetal Kidney	kidney
40	chr8:89337200-89341400	Active TSS	NHDF-Ad	bronchial
41	chr8:89337200-89341600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr8:89337400-89337800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr8:89337400-89337800	Flanking Active TSS	Fetal Brain Male	brain
44	chr8:89337400-89338000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr8:89337400-89341000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr8:89337400-89341600	Active TSS	NH-A	brain
47	chr8:89337600-89337800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr8:89337600-89337800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr8:89337600-89337800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr8:89337600-89337800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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