Variant report

Variant	rs828614
Chromosome Location	chr3:98538799-98538800
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	chr3:98537958-98539024	U87	brain:	n/a	n/a
2	POLR2A	chr3:98532422-98540691	U87	brain:	n/a	n/a
3	POLR2A	chr3:98531678-98540691	U87	brain:	n/a	n/a
4	POLR2A	chr3:98530977-98539024	U87	brain:	n/a	n/a
5	MYC	chr3:98538711-98538837	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935513	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10935514	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1095911	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632798	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12695786	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13081543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13316760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13319666	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1371687	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1967009	0.80[CHB][hapmap]
rs2062059	0.84[CHB][hapmap]
rs2333923	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439237	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs278376	0.92[CEU][hapmap];0.86[AMR][1000 genomes]
rs278379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278380	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278381	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278382	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278387	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278388	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278390	0.88[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35760367	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4546099	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4857415	0.81[EUR][1000 genomes]
rs6767370	0.81[EUR][1000 genomes]
rs6774875	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6791389	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7615628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828603	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs828605	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs828610	0.89[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs828616	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852701	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8833	0.88[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs955351	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9682876	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837206	0.85[EUR][1000 genomes]
rs9842522	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880179	0.85[EUR][1000 genomes];0.84[ASN][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs828614	DCBLD2	cis	Adipose Subcutaneous	GTEx
rs828614	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
3	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
4	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:98524200-98544200	Strong transcription	HSMM	muscle
7	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
8	chr3:98526200-98543200	Weak transcription	Lung	lung
9	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
11	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
14	chr3:98526600-98539000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
16	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:98528600-98543600	Strong transcription	NHEK	skin
22	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:98529000-98540000	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:98529400-98539000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:98530400-98542000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:98530800-98542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:98532400-98541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
30	chr3:98532800-98541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:98534000-98545000	Weak transcription	Ovary	ovary
32	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:98534200-98539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:98534200-98542800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:98534600-98544200	Strong transcription	HMEC	breast
38	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
39	chr3:98534800-98539600	Genic enhancers	A549	lung
40	chr3:98535200-98538800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:98535200-98540200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98535400-98541800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:98535400-98542600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr3:98535400-98543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:98535600-98538800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:98535600-98538800	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:98535600-98541600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:98535800-98538800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:98535800-98538800	Strong transcription	Left Ventricle	heart
50	chr3:98536000-98538800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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