Variant report

Variant	rs7649498
Chromosome Location	chr3:28391625-28391626
allele	A/C
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	chr3:28389421-28392084	GM12878	blood:	n/a	n/a
2	CUX1	chr3:28389078-28391644	K562	blood:	n/a	n/a
3	EP300	chr3:28389140-28391841	K562	blood:	n/a	chr3:28389265-28389279 chr3:28390526-28390533 chr3:28390482-28390498
4	POLR2A	chr3:28388873-28392054	IMR90	lung:	n/a	n/a
5	BRCA1	chr3:28389022-28391711	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:28388560-28395839	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr3:28391585-28391649	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:28388951-28391892	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:28388762-28392516	K562	blood:	n/a	n/a
10	POLR2A	chr3:28389004-28391702	K562	blood:	n/a	n/a
11	POLR2A	chr3:28387839-28396035	MCF10A-Er-Src	breast:	n/a	n/a
12	HCFC1	chr3:28388191-28391638	Hela-S3	cervix:	n/a	n/a
13	RCOR1	chr3:28389644-28391691	K562	blood:	n/a	n/a
14	IRF1	chr3:28388035-28391677	K562	blood:	n/a	chr3:28391536-28391549 chr3:28391382-28391398

No.	Distal block	Cell Line	Cell type
1	chr3:28360111..28361698-chr3:28390791..28393091,2	K562	blood:
2	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
3	chr3:28390959..28393888-chr3:28439197..28440878,2	K562	blood:
4	chr3:28391232..28393248-chr3:28418194..28419782,2	K562	blood:
5	chr3:23957644..23960053-chr3:28390990..28393934,2	K562	blood:
6	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
7	chr2:3621624..3624347-chr3:28389179..28391722,2	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000187118	Chromatin interaction
ENSG00000171863	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11706332	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11707705	1.00[CHB][hapmap]
rs11709034	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]
rs11712484	1.00[CHB][hapmap]
rs11712489	1.00[CHB][hapmap]
rs11720107	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs11918050	1.00[CHB][hapmap]
rs11921692	1.00[CHB][hapmap]
rs11921943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs12107256	0.85[CHB][hapmap]
rs13065010	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069839	0.89[ASN][1000 genomes]
rs13070434	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13075840	1.00[CHB][hapmap]
rs13081520	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs13082167	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13083544	0.85[CHB][hapmap]
rs13085075	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13087143	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13087774	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13088574	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13090296	0.85[CHB][hapmap]
rs13090439	1.00[CHB][hapmap]
rs13093242	0.85[CHB][hapmap]
rs13095628	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs13095675	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101128	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1457910	1.00[CHB][hapmap]
rs1585211	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1598846	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs1599826	0.92[CHB][hapmap]
rs1606386	0.92[CHB][hapmap]
rs1606388	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs1606393	0.92[CEU][hapmap];0.82[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];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs17638742	0.92[CHB][hapmap]
rs17638991	1.00[CHB][hapmap];0.80[CHD][hapmap]
rs17695765	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17695884	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17696025	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs17696459	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs17696783	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1870259	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975828	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1975829	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2018136	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2168799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34311197	0.80[ASN][1000 genomes]
rs34796684	0.82[ASN][1000 genomes]
rs35702956	0.82[ASN][1000 genomes]
rs36105900	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs3762797	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4327342	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4452283	1.00[CHB][hapmap]
rs4585155	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4680750	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680909	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]
rs4680910	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680913	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251131	0.82[ASN][1000 genomes]
rs62251134	0.82[ASN][1000 genomes]
rs62251138	0.80[ASN][1000 genomes]
rs66733194	0.80[ASN][1000 genomes]
rs6762636	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6763313	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771460	1.00[CHB][hapmap]
rs6777813	0.93[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs6788754	0.82[EUR][1000 genomes]
rs6803692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7434193	1.00[CHB][hapmap]
rs7639750	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641491	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643191	1.00[CHB][hapmap]
rs7650742	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7651883	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9310865	0.92[YRI][hapmap]
rs969443	1.00[CHB][hapmap]
rs9843464	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv2500136	chr3:28391396-28393792	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7649498	OSBPL10	cis	parietal	SCAN
rs7649498	RGS19	trans	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28387600-28392200	Active TSS	Right Atrium	heart
2	chr3:28388000-28392000	Active TSS	NHLF	lung
3	chr3:28388200-28391800	Active TSS	HMEC	breast
4	chr3:28388200-28392000	Active TSS	GM12878-XiMat	blood
5	chr3:28388200-28392000	Active TSS	K562	blood
6	chr3:28388400-28391800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:28388400-28392200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:28389000-28391800	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:28389200-28392200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:28389400-28391800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:28389800-28392000	Active TSS	Liver	Liver
12	chr3:28390800-28391800	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr3:28390800-28391800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr3:28391000-28391800	Flanking Active TSS	Dnd41	blood
15	chr3:28391000-28391800	Flanking Active TSS	HSMMtube	muscle
16	chr3:28391000-28391800	Flanking Active TSS	HUVEC	blood vessel
17	chr3:28391000-28391800	Flanking Active TSS	Osteobl	bone
18	chr3:28391000-28392200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:28391000-28394400	Weak transcription	Spleen	Spleen
20	chr3:28391200-28393600	Weak transcription	Gastric	stomach
21	chr3:28391200-28395200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:28391400-28391800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr3:28391400-28391800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:28391400-28391800	Enhancers	Brain Angular Gyrus	brain
25	chr3:28391400-28391800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:28391400-28391800	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr3:28391400-28391800	Enhancers	Fetal Heart	heart
28	chr3:28391400-28391800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr3:28391400-28391800	Enhancers	Rectal Smooth Muscle	rectum
30	chr3:28391400-28391800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr3:28391400-28391800	Flanking Active TSS	Hela-S3	cervix
32	chr3:28391400-28391800	Flanking Active TSS	NHEK	skin
33	chr3:28391400-28392000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:28391400-28392000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:28391400-28392000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:28391400-28392200	Enhancers	Brain Anterior Caudate	brain
37	chr3:28391400-28392400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:28391400-28392800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr3:28391400-28393200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:28391400-28393200	Weak transcription	Fetal Kidney	kidney
41	chr3:28391400-28393200	Weak transcription	Ovary	ovary
42	chr3:28391400-28393600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:28391400-28393600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:28391400-28393600	Weak transcription	Aorta	Aorta
45	chr3:28391400-28393600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:28391400-28393600	Weak transcription	Pancreas	Pancrea
47	chr3:28391400-28393600	Weak transcription	HSMM	muscle
48	chr3:28391400-28394000	Weak transcription	Brain Substantia Nigra	brain
49	chr3:28391400-28394200	Weak transcription	Left Ventricle	heart
50	chr3:28391400-28394400	Weak transcription	Placenta	Placenta

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