Variant report

Variant	rs4680909
Chromosome Location	chr3:28356457-28356458
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	chr3:28354963-28357746	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:28339558..28341827-chr3:28352714..28356696,3	K562	blood:
2	chr3:28355500..28357413-chr3:28388215..28391040,2	MCF-7	breast:
3	chr3:28339828..28341827-chr3:28353831..28356696,2	K562	blood:

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000206559	Chromatin interaction
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11706332	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs11707705	1.00[CHB][hapmap]
rs11709034	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]
rs11712484	1.00[CHB][hapmap]
rs11712489	1.00[CHB][hapmap]
rs11720107	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs11918050	1.00[CHB][hapmap]
rs11921692	1.00[CHB][hapmap]
rs11921943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12107256	0.85[CHB][hapmap]
rs13065010	0.86[EUR][1000 genomes]
rs13070434	0.81[EUR][1000 genomes]
rs13075840	1.00[CHB][hapmap]
rs13081520	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13082167	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13083544	0.85[CHB][hapmap]
rs13085075	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087143	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13087774	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13088574	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs13090296	0.85[CHB][hapmap]
rs13090439	1.00[CHB][hapmap]
rs13093242	0.85[CHB][hapmap]
rs13095628	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13095675	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13101128	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1457910	1.00[CHB][hapmap]
rs1585211	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1598846	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1599826	0.92[CHB][hapmap]
rs1606386	0.92[CHB][hapmap]
rs1606388	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs1606393	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs1610238	0.85[CHB][hapmap]
rs17021221	0.85[CHB][hapmap]
rs17021306	0.85[CHB][hapmap]
rs17021402	1.00[CHB][hapmap]
rs17357206	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17638742	0.92[CHB][hapmap]
rs17638991	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs17695765	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs17695884	1.00[CHB][hapmap]
rs17696025	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17696459	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17696783	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs1870259	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1975828	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1975829	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2018136	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2168799	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34574968	0.80[ASN][1000 genomes]
rs36105900	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs3762797	1.00[CHB][hapmap]
rs4327342	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4452283	1.00[CHB][hapmap]
rs4585155	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680750	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680910	0.84[ASN][1000 genomes]
rs4680913	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62251105	0.80[ASN][1000 genomes]
rs6762636	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763313	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6771057	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6771460	1.00[CHB][hapmap]
rs6803692	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7434193	1.00[CHB][hapmap]
rs7639750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7641491	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643191	1.00[CHB][hapmap]
rs7649498	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7650742	0.81[EUR][1000 genomes]
rs7651883	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs969443	1.00[CHB][hapmap]
rs9843464	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680909	RGS19	trans	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:28315000-28363000	Weak transcription	A549	lung
3	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
5	chr3:28326400-28365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:28332800-28360000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:28332800-28360200	Weak transcription	Left Ventricle	heart
8	chr3:28332800-28360400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:28332800-28362400	Weak transcription	Primary B cells from cord blood	blood
10	chr3:28332800-28365200	Weak transcription	HSMMtube	muscle
11	chr3:28332800-28365400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:28336800-28359400	Weak transcription	K562	blood
13	chr3:28337200-28365200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:28337400-28360400	Weak transcription	Liver	Liver
15	chr3:28337400-28361000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:28337400-28363000	Weak transcription	GM12878-XiMat	blood
17	chr3:28337600-28356600	Weak transcription	Ovary	ovary
18	chr3:28337600-28360200	Weak transcription	Fetal Lung	lung
19	chr3:28337600-28360200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:28337600-28361000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:28338000-28359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:28338000-28360200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:28338000-28360600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:28338200-28364000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:28339600-28359200	Weak transcription	Dnd41	blood
26	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
27	chr3:28347400-28360000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:28348600-28360000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:28348600-28365200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:28349000-28365400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:28349400-28364200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:28349400-28365600	Weak transcription	Psoas Muscle	Psoas
33	chr3:28349600-28365400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:28349800-28359800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:28349800-28389400	Weak transcription	Gastric	stomach
36	chr3:28350000-28359600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:28350000-28363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:28350200-28361600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:28350400-28365400	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:28350600-28360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:28351200-28366600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:28351400-28365600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:28351400-28366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr3:28352800-28360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:28353200-28360200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:28354200-28364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:28354800-28363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:28354800-28365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:28355200-28360600	Weak transcription	Primary monocytes fromperipheralblood	blood

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