Variant report

Variant	rs12676684
Chromosome Location	chr8:118857704-118857705
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:118855769..118857808-chr8:118858590..118860796,2	MCF-7	breast:
2	8:118854388-118858307..8:119119523-119124860	GM12878	blood:

Variant related genes	Relation type
ENSG00000182197	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10089630	0.83[CEU][hapmap]
rs10098795	0.83[CEU][hapmap]
rs10955836	0.82[CEU][hapmap]
rs12677136	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs12680472	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12682457	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17430315	0.83[CEU][hapmap]
rs17430357	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17430364	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17439784	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17439826	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17450709	0.83[CHB][hapmap]
rs17450758	0.81[CHB][hapmap]
rs17452847	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs4129114	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs66732486	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7000499	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019636	chr8:118598433-118946091	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv539734	chr8:118598433-118946091	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831439	chr8:118747352-118899118	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv933516	chr8:118764605-119009093	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1030459	chr8:118840179-119155835	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12676684	DEPDC6	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:118825200-118859600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:118825200-118859800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:118825400-118859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:118825600-118860000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr8:118829800-118859800	Weak transcription	Esophagus	oesophagus
6	chr8:118832600-118859800	Weak transcription	Spleen	Spleen
7	chr8:118835000-118859600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:118835000-118859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr8:118845400-118859600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:118846600-118861800	Weak transcription	HUVEC	blood vessel
11	chr8:118848000-118859800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr8:118848200-118859600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr8:118848400-118859800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:118848800-118858000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:118849000-118859000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr8:118849200-118859000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr8:118849400-118859000	Weak transcription	Fetal Stomach	stomach
18	chr8:118849600-118865800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr8:118849800-118859200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:118850600-118859800	Weak transcription	A549	lung
21	chr8:118852800-118858800	Weak transcription	Fetal Muscle Leg	muscle
22	chr8:118853400-118859200	Weak transcription	Brain Anterior Caudate	brain
23	chr8:118853600-118858400	Weak transcription	Fetal Brain Male	brain
24	chr8:118853600-118860000	Weak transcription	Right Ventricle	heart
25	chr8:118853800-118859400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:118853800-118861200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr8:118854200-118858000	Weak transcription	Fetal Heart	heart
28	chr8:118855200-118858800	Weak transcription	HSMM	muscle
29	chr8:118855200-118859400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr8:118855200-118859400	Weak transcription	HMEC	breast
31	chr8:118855200-118859800	Weak transcription	Psoas Muscle	Psoas
32	chr8:118855400-118859400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr8:118855600-118859400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr8:118855800-118858000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr8:118855800-118858800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr8:118855800-118859000	Weak transcription	Lung	lung
37	chr8:118855800-118859000	Weak transcription	Ovary	ovary
38	chr8:118855800-118859600	Weak transcription	Colon Smooth Muscle	Colon
39	chr8:118855800-118859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr8:118855800-118859800	Weak transcription	Gastric	stomach
41	chr8:118855800-118862400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr8:118855800-118866200	Weak transcription	Liver	Liver
43	chr8:118856000-118858200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:118856200-118858000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:118856200-118858600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:118856200-118859000	Weak transcription	Osteobl	bone
47	chr8:118856200-118859200	Weak transcription	NH-A	brain
48	chr8:118856200-118859200	Weak transcription	NHDF-Ad	bronchial
49	chr8:118856600-118858400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr8:118856800-118858200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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