Variant report

Variant	rs828610
Chromosome Location	chr3:98501603-98501604
allele	C/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	chr3:98500239-98520630	U87	brain:	n/a	n/a
2	WRNIP1	chr3:98501474-98501632	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
4	EP300	chr3:98501557-98502433	ECC-1	luminal epithelium:	n/a	chr3:98502310-98502324
5	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10935514	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs1095911	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12632798	0.96[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap]
rs12636683	0.92[EUR][1000 genomes]
rs13071075	0.88[EUR][1000 genomes]
rs13316760	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs1371687	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2333923	0.81[EUR][1000 genomes]
rs2439237	1.00[JPT][hapmap]
rs278376	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs278379	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs278380	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278381	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278382	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278387	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278388	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs278390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4857415	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6767370	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6774875	0.90[JPT][hapmap]
rs6791389	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7615628	0.95[JPT][hapmap]
rs7615856	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs828603	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828605	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828614	0.89[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs828616	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]
rs828617	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs828618	0.84[CEU][hapmap]
rs828621	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs852701	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8833	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs955351	0.88[CEU][hapmap];0.90[JPT][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs828610	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx
rs828610	DCBLD2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:98494600-98506000	Enhancers	Aorta	Aorta
14	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
16	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
17	chr3:98497400-98501800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98497400-98503600	Enhancers	Placenta	Placenta
19	chr3:98497600-98502400	Weak transcription	Lung	lung
20	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
21	chr3:98498000-98501800	Weak transcription	Gastric	stomach
22	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
24	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
25	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
26	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
27	chr3:98498800-98502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:98499000-98504200	Weak transcription	HSMM	muscle
33	chr3:98499200-98501800	Weak transcription	NHEK	skin
34	chr3:98499200-98502200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
36	chr3:98499200-98503400	Weak transcription	NHLF	lung
37	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
41	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:98499600-98502000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:98499600-98502000	Weak transcription	Fetal Intestine Large	intestine
45	chr3:98499600-98502200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:98499600-98503000	Weak transcription	Adipose Nuclei	Adipose
47	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:98499800-98501800	Weak transcription	Osteobl	bone
50	chr3:98499800-98502200	Weak transcription	Brain Anterior Caudate	brain

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