Variant report

Variant	rs828616
Chromosome Location	chr3:98541116-98541117
allele	A/G
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	chr3:98539036-98544468	U87	brain:	n/a	n/a
2	POLR2A	chr3:98540794-98541814	U87	brain:	n/a	n/a
3	POLR2A	chr3:98540774-98541835	U87	brain:	n/a	n/a
4	POLR2A	chr3:98539030-98544468	U87	brain:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10935514	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1095911	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632798	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636683	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13071075	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081543	0.80[EUR][1000 genomes]
rs13316760	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1371687	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1383906	0.81[EUR][1000 genomes]
rs1383907	0.81[EUR][1000 genomes]
rs2333923	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2340794	0.81[EUR][1000 genomes]
rs2439237	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2449046	0.80[EUR][1000 genomes]
rs2470873	0.81[EUR][1000 genomes]
rs2470877	0.81[EUR][1000 genomes]
rs2470880	0.80[EUR][1000 genomes]
rs278376	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs278379	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278380	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278381	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278382	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278387	0.82[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278388	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278390	0.82[ASW][hapmap];0.88[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35483904	0.82[EUR][1000 genomes]
rs35760367	0.81[EUR][1000 genomes]
rs35936923	0.81[EUR][1000 genomes]
rs4577404	0.83[EUR][1000 genomes]
rs4857415	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767370	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6774875	0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6791389	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615628	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7615856	0.88[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs828603	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs828605	0.82[ASW][hapmap];0.92[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828610	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs828614	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	0.87[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828621	0.87[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]
rs852701	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8833	0.82[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs955351	0.84[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs828616	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs828616	DCBLD2	cis	Adipose Subcutaneous	GTEx
rs828616	ZBTB11	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
3	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:98524200-98544200	Strong transcription	HSMM	muscle
6	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
7	chr3:98526200-98543200	Weak transcription	Lung	lung
8	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
10	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:98528600-98543600	Strong transcription	NHEK	skin
17	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:98530400-98542000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:98530800-98542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:98532400-98541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
23	chr3:98532800-98541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:98534000-98545000	Weak transcription	Ovary	ovary
25	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:98534200-98542800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:98534600-98544200	Strong transcription	HMEC	breast
30	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
31	chr3:98535400-98541800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:98535400-98542600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr3:98535400-98543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:98535600-98541600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:98536000-98542000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:98536000-98542800	Strong transcription	NH-A	brain
37	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
38	chr3:98536200-98542600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:98536200-98542600	Weak transcription	Fetal Stomach	stomach
40	chr3:98536200-98594200	Weak transcription	HepG2	liver
41	chr3:98536800-98543000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:98536800-98545000	Weak transcription	Fetal Kidney	kidney
43	chr3:98537000-98541400	Strong transcription	HUVEC	blood vessel
44	chr3:98537000-98542600	Weak transcription	Dnd41	blood
45	chr3:98537000-98542600	Strong transcription	Osteobl	bone
46	chr3:98537000-98545600	Weak transcription	HSMMtube	muscle
47	chr3:98537000-98546200	Weak transcription	Brain Anterior Caudate	brain
48	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:98537000-98592800	Weak transcription	K562	blood
50	chr3:98537400-98551200	Weak transcription	Fetal Heart	heart

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