Variant report

Variant	rs6680578
Chromosome Location	chr1:93176878-93176879
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93175208..93177703-chr1:93227101..93229847,2	K562	blood:
2	chr1:93175257..93178526-chr1:93178760..93181629,3	K562	blood:
3	chr1:93164366..93166063-chr1:93176534..93179501,2	K562	blood:
4	chr1:93168714..93171281-chr1:93175586..93177919,2	K562	blood:

Extended variants
information (count: 207 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:203)

rs_ID	r²[population]
rs1003116	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10218670	0.82[CHB][hapmap]
rs1034218	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1034219	0.82[CHB][hapmap]
rs10735779	0.82[CHB][hapmap]
rs10735781	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10735782	0.82[CHB][hapmap]
rs10747445	0.82[CHB][hapmap]
rs10747446	0.86[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10747448	0.82[CHB][hapmap]
rs10747449	0.82[CHB][hapmap]
rs10747450	0.82[CHB][hapmap]
rs10782936	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10782937	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782940	0.82[CHB][hapmap]
rs10782941	0.89[EUR][1000 genomes]
rs10782945	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10782946	1.00[JPT][hapmap]
rs10874710	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10874711	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10874715	0.82[CHB][hapmap]
rs10874716	0.82[CHB][hapmap]
rs10874724	0.83[EUR][1000 genomes]
rs10874725	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10874726	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10874727	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10874728	0.82[CHB][hapmap]
rs10874729	0.82[CHB][hapmap]
rs10874731	0.82[CHB][hapmap]
rs10874732	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10874733	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10874736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874738	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10874744	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10874746	1.00[JPT][hapmap]
rs10874747	1.00[JPT][hapmap]
rs11164778	0.82[CHB][hapmap]
rs11164785	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11164789	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11164791	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164796	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11164804	0.82[CHB][hapmap]
rs11164807	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11164808	0.82[CHB][hapmap]
rs11164810	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12021539	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12025792	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12046739	0.82[CHB][hapmap]
rs12123935	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12401423	0.84[EUR][1000 genomes]
rs1337107	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1337109	0.82[CHB][hapmap]
rs1408916	0.82[CHB][hapmap]
rs1415294	0.82[CHB][hapmap]
rs1415295	0.82[CHB][hapmap]
rs1535372	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1537498	0.82[CHB][hapmap]
rs1538029	0.82[CHB][hapmap]
rs1556562	0.82[CHB][hapmap]
rs1556564	0.82[CHB][hapmap]
rs1556565	0.82[CHB][hapmap]
rs1570837	0.82[CHB][hapmap]
rs1886682	0.82[CHB][hapmap]
rs1932965	1.00[CHB][hapmap]
rs1932966	0.82[CHB][hapmap]
rs2027059	0.82[CHB][hapmap]
rs2027060	0.82[CHB][hapmap]
rs2039452	0.82[CHB][hapmap]
rs2050597	0.82[CHB][hapmap]
rs2065915	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2065916	0.82[CHB][hapmap]
rs2095268	0.82[CHB][hapmap]
rs2107518	0.89[EUR][1000 genomes]
rs2107519	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107520	0.82[CHB][hapmap]
rs2107521	0.82[CHB][hapmap]
rs2151577	0.82[CHB][hapmap]
rs2158446	0.82[CHB][hapmap]
rs2180977	0.82[CHB][hapmap]
rs2255717	1.00[JPT][hapmap]
rs2391164	0.82[CHB][hapmap]
rs2391196	0.82[CHB][hapmap]
rs2391197	0.92[EUR][1000 genomes]
rs2391199	0.82[CHB][hapmap]
rs2481710	1.00[JPT][hapmap]
rs2774953	1.00[JPT][hapmap]
rs2811594	1.00[JPT][hapmap]
rs2893217	0.82[CHB][hapmap]
rs35054144	0.82[CHB][hapmap]
rs3790445	0.82[CHB][hapmap]
rs3790446	0.82[CHB][hapmap]
rs3903212	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs3928821	0.82[CHB][hapmap]
rs3936944	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3936945	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs3936946	1.00[CHB][hapmap]
rs4294422	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4294424	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4480368	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4568842	0.82[CHB][hapmap]
rs4847181	0.82[CHB][hapmap]
rs4847232	0.82[CHB][hapmap]
rs4847247	0.82[CHB][hapmap]
rs4847266	0.82[CHB][hapmap]
rs4847267	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4847280	0.82[CHB][hapmap]
rs4847301	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847305	0.82[CHB][hapmap]
rs4847306	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4847311	0.84[EUR][1000 genomes]
rs4847327	0.82[CHB][hapmap]
rs4847336	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4847377	0.82[CHB][hapmap]
rs4847378	1.00[JPT][hapmap]
rs4847432	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4970707	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4970709	0.82[CHB][hapmap]
rs4970710	0.82[CHB][hapmap]
rs4970712	0.82[CHB][hapmap]
rs6422512	0.82[CHB][hapmap]
rs6422515	0.82[CHB][hapmap]
rs6603979	0.82[CHB][hapmap]
rs6603981	0.82[CHB][hapmap]
rs6603982	0.82[CHB][hapmap]
rs6603984	0.82[CHB][hapmap]
rs6603985	0.82[CHB][hapmap]
rs6603986	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap]
rs6603987	0.82[CHB][hapmap]
rs6603988	0.82[CHB][hapmap]
rs6603989	0.82[EUR][1000 genomes]
rs6603990	0.82[CHB][hapmap]
rs6603992	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6603993	0.82[CHB][hapmap]
rs6603994	0.82[CHB][hapmap]
rs6603995	0.82[CHB][hapmap]
rs6603997	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6603999	0.82[CHB][hapmap]
rs6604003	0.82[CHB][hapmap]
rs6604007	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6604008	0.94[EUR][1000 genomes]
rs6604010	0.82[CHB][hapmap]
rs6604013	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6604014	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6604015	0.82[CHB][hapmap]
rs6604018	0.82[CHB][hapmap]
rs6660136	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6660962	0.82[EUR][1000 genomes]
rs6661600	0.82[CHB][hapmap]
rs6666831	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671114	0.82[CHB][hapmap]
rs6671421	0.82[CHB][hapmap]
rs6675246	0.82[CHB][hapmap]
rs6675753	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675757	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682801	0.86[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6685705	0.82[CHB][hapmap]
rs6692187	0.82[CHB][hapmap]
rs6695638	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6696173	0.82[CHB][hapmap]
rs6696636	0.82[CHB][hapmap]
rs6697491	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6701130	0.82[CHB][hapmap]
rs6703467	0.82[CHB][hapmap]
rs722356	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7416169	0.82[CHB][hapmap]
rs7417452	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7418336	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7513775	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7513815	0.82[CHB][hapmap]
rs7514334	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7514716	0.82[CHB][hapmap]
rs7515577	0.82[CHB][hapmap]
rs7516141	0.82[CHB][hapmap]
rs7521752	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7526582	0.82[CHB][hapmap]
rs7529332	0.82[CHB][hapmap]
rs7529630	0.82[CHB][hapmap]
rs7530780	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7535490	0.84[EUR][1000 genomes]
rs7536563	1.00[JPT][hapmap]
rs7539761	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7540407	0.82[CHB][hapmap]
rs7541588	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7541942	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7543327	0.82[CHB][hapmap]
rs7545318	0.82[CHB][hapmap]
rs7546197	0.93[EUR][1000 genomes]
rs7549341	0.84[EUR][1000 genomes]
rs7549844	0.82[CHB][hapmap]
rs7551324	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7553367	0.82[CHB][hapmap]
rs7556243	0.82[CHB][hapmap]
rs911523	0.92[EUR][1000 genomes]
rs914966	0.82[CHB][hapmap]
rs927339	0.82[CHB][hapmap]
rs932637	0.82[CHB][hapmap]
rs9439920	0.82[CHB][hapmap]
rs945724	0.82[CHB][hapmap]
rs963043	0.82[CHB][hapmap]
rs963044	0.82[CHB][hapmap]
rs9651256	0.82[CHB][hapmap]
rs976208	0.82[CHB][hapmap]
rs989653	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794348	chr1:93090476-93192932	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv997898	chr1:93167128-93228156	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6680578	MTF2	cis	cerebellum	SCAN
rs6680578	EPHX4	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93098400-93205400	Weak transcription	NHLF	lung
2	chr1:93123600-93178800	Weak transcription	Aorta	Aorta
3	chr1:93123600-93213400	Weak transcription	Gastric	stomach
4	chr1:93155800-93213400	Weak transcription	Lung	lung
5	chr1:93160800-93177000	Weak transcription	Ovary	ovary
6	chr1:93161000-93197400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:93161000-93197800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:93161000-93199000	Weak transcription	Left Ventricle	heart
9	chr1:93163800-93177400	Weak transcription	Placenta	Placenta
10	chr1:93163800-93190000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:93167600-93177800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr1:93170200-93189800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:93171400-93177400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:93173400-93177800	Enhancers	K562	blood
15	chr1:93174200-93177000	Enhancers	Liver	Liver
16	chr1:93174400-93202000	Weak transcription	Fetal Heart	heart
17	chr1:93175200-93177800	Enhancers	Fetal Intestine Large	intestine
18	chr1:93175200-93178000	Enhancers	HepG2	liver
19	chr1:93175200-93178400	Enhancers	Fetal Intestine Small	intestine
20	chr1:93175400-93177600	Enhancers	Pancreas	Pancrea
21	chr1:93175600-93177800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:93175600-93177800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:93175600-93179400	Weak transcription	A549	lung
24	chr1:93175600-93180000	Weak transcription	Stomach Mucosa	stomach
25	chr1:93175800-93190200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:93175800-93199400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:93176000-93177000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:93176000-93183200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:93176200-93177000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:93176200-93177400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:93176400-93177600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:93176600-93177400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:93176800-93177200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:93176800-93177400	Enhancers	Colon Smooth Muscle	Colon
35	chr1:93176800-93177600	Enhancers	Psoas Muscle	Psoas

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