Variant report

Variant	rs16893478
Chromosome Location	chr8:121073254-121073255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:120883686..120886465-chr8:121071792..121074526,2	MCF-7	breast:
2	chr8:120992487..120993376-chr8:121072550..121073500,6	MCF-7	breast:
3	chr8:120886386..120887290-chr8:121072685..121073939,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245330	Chromatin interaction
ENSG00000155792	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10090001	0.92[EUR][1000 genomes]
rs10095205	0.84[EUR][1000 genomes]
rs10095532	0.84[EUR][1000 genomes]
rs10101620	0.92[EUR][1000 genomes]
rs10101943	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs10505376	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10955948	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1120223	0.88[EUR][1000 genomes]
rs11780912	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11780985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12114445	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12542895	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543907	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12545676	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12548223	0.90[JPT][hapmap]
rs12548273	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1519807	0.90[EUR][1000 genomes]
rs1519808	0.90[EUR][1000 genomes]
rs1519812	0.85[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs1519813	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16893517	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893536	0.80[JPT][hapmap]
rs16893570	0.80[JPT][hapmap]
rs17226296	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17822044	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1980228	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs2292946	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs28530768	0.84[EUR][1000 genomes]
rs2875928	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2875931	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871825	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4871828	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56702755	0.87[EUR][1000 genomes]
rs57868486	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60717250	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60754245	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469894	0.90[EUR][1000 genomes]
rs6469895	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469897	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66490854	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66507952	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66614869	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67872361	0.82[EUR][1000 genomes]
rs6980708	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs6981402	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6986231	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6993924	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6998730	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7000436	0.85[YRI][hapmap]
rs7004815	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7005228	0.92[EUR][1000 genomes]
rs7007998	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013298	0.96[CEU][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs7016816	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72675741	1.00[ASN][1000 genomes]
rs73315941	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7816925	0.80[JPT][hapmap]
rs7817016	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs7821947	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7822662	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7822927	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829101	0.80[CEU][hapmap];0.84[CHD][hapmap];0.84[EUR][1000 genomes]
rs7829116	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7830028	0.84[EUR][1000 genomes]
rs7833073	0.96[CEU][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs7836087	0.96[CEU][hapmap];0.84[CHD][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7840217	0.80[JPT][hapmap]
rs7841230	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7843503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs955293	0.85[CEU][hapmap];0.88[CHD][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs960887	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[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	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS 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	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16893478	DEPDC6	cis	normal skin	skin_eQTL
rs16893478	DEPDC6	cis	uninvolved skin	skin_eQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121059400-121077800	Weak transcription	Fetal Stomach	stomach
2	chr8:121060600-121085000	Weak transcription	Fetal Muscle Leg	muscle
3	chr8:121064200-121074800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr8:121064400-121077200	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:121064400-121077600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr8:121064600-121077200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:121066400-121074800	Weak transcription	Gastric	stomach
8	chr8:121069600-121077400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr8:121070800-121082200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr8:121071200-121074000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr8:121072600-121073400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:121072600-121073400	Enhancers	HMEC	breast
13	chr8:121072600-121073600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:121072600-121073600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr8:121072600-121073600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:121072600-121073600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:121072600-121073600	Enhancers	NHEK	skin
18	chr8:121072600-121074200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:121072600-121074400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:121072600-121077200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr8:121072800-121073400	Enhancers	Primary hematopoietic stem cells	blood
22	chr8:121072800-121073400	Enhancers	Brain Cingulate Gyrus	brain
23	chr8:121072800-121073400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr8:121072800-121073400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr8:121072800-121073400	Enhancers	Stomach Mucosa	stomach
26	chr8:121072800-121073400	Enhancers	Stomach Smooth Muscle	stomach
27	chr8:121072800-121073400	Enhancers	A549	lung
28	chr8:121072800-121073600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:121072800-121073600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr8:121072800-121073600	Enhancers	Brain Substantia Nigra	brain
31	chr8:121072800-121073600	Enhancers	Colon Smooth Muscle	Colon
32	chr8:121072800-121073600	Enhancers	Rectal Smooth Muscle	rectum
33	chr8:121072800-121073600	Enhancers	HSMMtube	muscle
34	chr8:121072800-121073600	Enhancers	Osteobl	bone
35	chr8:121072800-121074000	Enhancers	Brain Angular Gyrus	brain
36	chr8:121072800-121074200	Enhancers	Fetal Kidney	kidney
37	chr8:121072800-121078000	Enhancers	Liver	Liver
38	chr8:121073000-121073400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr8:121073000-121074200	Enhancers	Fetal Intestine Large	intestine
40	chr8:121073000-121074200	Enhancers	Fetal Intestine Small	intestine
41	chr8:121073200-121073600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr8:121073200-121077200	Weak transcription	Fetal Lung	lung
43	chr8:121073200-121077400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr8:121073200-121077400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr8:121073200-121080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr8:121073200-121080800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr8:121073200-121081400	Weak transcription	Psoas Muscle	Psoas

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