Variant report

Variant	rs11709034
Chromosome Location	chr3:28332087-28332088
allele	G/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	chr3:28331633-28332246	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28282547..28284660-chr3:28329790..28333185,3	K562	blood:
2	chr3:28330659..28335850-chr3:28336340..28340116,5	K562	blood:

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11921943	0.89[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs13085075	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13095675	0.81[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap]
rs13101128	0.91[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1585211	0.94[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1606393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870259	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1975829	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2168799	0.82[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs4585155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680909	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680913	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs6762636	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6771057	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6803692	0.92[CEU][hapmap]
rs7639750	0.89[CEU][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7641491	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7649498	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7651883	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs9843464	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11709034	OSBPL10	cis	parietal	SCAN
rs11709034	RGS19	trans	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28303600-28340600	Weak transcription	NHEK	skin
2	chr3:28304200-28332400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:28306400-28332400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:28306600-28335800	Weak transcription	Hela-S3	cervix
5	chr3:28309000-28336600	Weak transcription	HUVEC	blood vessel
6	chr3:28314200-28332400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:28314400-28332400	Weak transcription	Ovary	ovary
8	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:28314600-28332600	Weak transcription	Left Ventricle	heart
10	chr3:28314800-28343400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:28315000-28332400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:28315000-28333000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:28315000-28363000	Weak transcription	A549	lung
14	chr3:28315200-28332200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:28315600-28332400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:28315600-28332400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:28315600-28332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:28315800-28332200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:28315800-28332200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:28315800-28332400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:28316200-28333200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:28317200-28332200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:28317400-28332400	Weak transcription	HSMM	muscle
24	chr3:28317400-28337200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:28317600-28332200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:28317600-28332400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:28317600-28332400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:28317600-28332400	Weak transcription	Lung	lung
29	chr3:28317600-28332400	Weak transcription	Thymus	Thymus
30	chr3:28317600-28337000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:28317600-28337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:28317600-28337200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:28317600-28337600	Weak transcription	Fetal Intestine Large	intestine
34	chr3:28317600-28341200	Weak transcription	Fetal Thymus	thymus
35	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
37	chr3:28317800-28332400	Weak transcription	Fetal Stomach	stomach
38	chr3:28317800-28332400	Weak transcription	Right Ventricle	heart
39	chr3:28317800-28337200	Weak transcription	Fetal Intestine Small	intestine
40	chr3:28317800-28343000	Weak transcription	HepG2	liver
41	chr3:28318600-28332200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:28321800-28332200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:28321800-28332400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:28322000-28336600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:28322600-28336400	Weak transcription	NHLF	lung
46	chr3:28322600-28340200	Weak transcription	Small Intestine	intestine
47	chr3:28326400-28365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:28328200-28337000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:28328200-28340800	Weak transcription	Fetal Heart	heart
50	chr3:28328400-28332400	Weak transcription	Adipose Nuclei	Adipose

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