Variant report

Variant	rs1886684
Chromosome Location	chr1:92975938-92975939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92975440..92978255-chr1:92987459..92989945,2	K562	blood:
2	chr1:92970721..92973129-chr1:92975876..92977774,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1003116	0.91[CEU][hapmap]
rs1034218	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1059267	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059268	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735781	0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs10747446	1.00[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs10782912	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10782936	1.00[CEU][hapmap];0.95[CHD][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782937	0.86[EUR][1000 genomes]
rs10874710	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874711	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10874724	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874725	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10874726	0.88[EUR][1000 genomes]
rs10874727	0.95[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs11164601	0.93[EUR][1000 genomes]
rs11164607	0.95[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs11164608	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs11164785	0.87[EUR][1000 genomes]
rs11164789	0.82[EUR][1000 genomes]
rs11164791	0.95[CEU][hapmap]
rs11164796	0.91[CEU][hapmap]
rs12025792	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1325434	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359490	0.95[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs35029291	0.81[EUR][1000 genomes]
rs3903212	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3936944	0.87[EUR][1000 genomes]
rs3936945	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs4000736	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4294422	0.95[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4294424	0.95[CEU][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs4484938	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565725	0.92[EUR][1000 genomes]
rs4847267	0.91[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap]
rs4847432	0.95[CEU][hapmap]
rs4970700	0.95[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs4970702	0.95[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs4970703	0.92[EUR][1000 genomes]
rs4970707	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970714	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs6603976	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603986	0.95[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6603989	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6603992	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6603997	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6604007	0.90[CEU][hapmap]
rs6660962	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6682801	1.00[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6695638	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6697491	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703440	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722356	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7417452	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7418336	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs7513775	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7514156	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514334	0.84[EUR][1000 genomes]
rs7520630	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7521752	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530780	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs7535490	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7540564	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541942	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs912796	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942753	0.95[CEU][hapmap];0.87[TSI][hapmap];0.92[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	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1004381	chr1:92968173-93064823	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1886684	EPHX4	cis	parietal	SCAN
rs1886684	FAM69A	cis	cerebellum	SCAN
rs1886684	MTF2	cis	cerebellum	SCAN
rs1886684	RPL5	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92952800-92991400	Weak transcription	Pancreas	Pancrea
2	chr1:92967800-92978400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:92967800-92986000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:92968200-92977400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:92968200-93042800	Weak transcription	HSMM	muscle
6	chr1:92968400-92997600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:92969400-92979800	Weak transcription	HSMMtube	muscle
8	chr1:92969600-92984200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:92969800-92992000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:92969800-92996800	Weak transcription	NH-A	brain
11	chr1:92970000-92992200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:92970600-92981800	Weak transcription	Primary B cells from cord blood	blood
13	chr1:92970800-92977200	Weak transcription	GM12878-XiMat	blood
14	chr1:92970800-92978800	Weak transcription	Placenta	Placenta
15	chr1:92971400-92978600	Weak transcription	Liver	Liver
16	chr1:92971400-92998600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:92972600-93013400	Weak transcription	Ovary	ovary
18	chr1:92973000-92983800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:92973400-92987400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:92973800-92997600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:92973800-93002200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:92975200-92979600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:92975200-92980600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:92975600-92980400	Weak transcription	Dnd41	blood

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