Variant report

Variant	rs6657284
Chromosome Location	chr1:45879088-45879089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1006216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1007858	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1084166	0.82[EUR][1000 genomes]
rs10890327	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890330	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs11211101	0.82[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[ASN][1000 genomes]
rs11211108	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211117	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211118	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211124	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs12029322	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs12037201	0.83[EUR][1000 genomes]
rs12037411	0.87[ASN][1000 genomes]
rs12046816	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12049503	0.86[CEU][hapmap];0.81[CHB][hapmap];0.81[MEX][hapmap]
rs12067642	0.80[ASN][1000 genomes]
rs12097497	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12410493	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1494812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17395553	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1771551	0.95[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.85[EUR][1000 genomes]
rs1826691	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2050884	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2055145	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs2088100	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2153607	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2153608	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2153609	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs2185549	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs2298018	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs2487442	0.87[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2492840	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs28555082	0.83[EUR][1000 genomes]
rs3219463	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs3219472	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap]
rs3219489	0.91[CEU][hapmap]
rs3790582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4520450	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap]
rs4633317	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4660849	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs4660851	0.95[CEU][hapmap]
rs4660852	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[ASN][1000 genomes]
rs4660853	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap]
rs4660854	0.91[CEU][hapmap]
rs4660855	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660858	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4660863	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs55642258	0.80[ASN][1000 genomes]
rs61788261	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788262	0.84[ASN][1000 genomes]
rs61788281	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61788285	0.80[ASN][1000 genomes]
rs61791368	0.85[ASN][1000 genomes]
rs61791369	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs713358	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs72686460	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7525849	0.82[EUR][1000 genomes]
rs7528573	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7531253	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7532762	0.87[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs7536135	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543428	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap]
rs7544178	0.82[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap]
rs7553318	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs781226	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs781230	0.85[EUR][1000 genomes]
rs781232	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs868351	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[TSI][hapmap]
rs884962	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs9326141	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9429072	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs9429076	0.95[CEU][hapmap]
rs9429158	0.91[CEU][hapmap]
rs9429159	0.80[ASN][1000 genomes]
rs9429160	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6657284	IPP	cis	lymphoblastoid	seeQTL
rs6657284	CLDN19	cis	cerebellum	SCAN
rs6657284	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs6657284	C2orf49	trans	lymphoblastoid	RTeQTL
rs6657284	TESK2	cis	Whole Blood	GTEx
rs6657284	MMACHC	cis	multi-tissue	Pritchard
rs6657284	GPBP1L1	cis	Lymphoblastoid	GTEx
rs6657284	Hs.396207	cis	multi-tissue	Pritchard
rs6657284	MAST2	cis	cerebellum	SCAN
rs6657284	IPP	cis	Lymphoblastoid	GTEx
rs6657284	ST3GAL3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45869400-45885400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:45875600-45889400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:45876600-45880000	Enhancers	Primary B cells from cord blood	blood
5	chr1:45876600-45880400	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:45876600-45881600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:45876800-45879200	Enhancers	GM12878-XiMat	blood
8	chr1:45876800-45887800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:45877000-45886800	Weak transcription	Liver	Liver
10	chr1:45877200-45887800	Weak transcription	Fetal Intestine Large	intestine
11	chr1:45877200-45888200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:45877400-45886800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:45877400-45889200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:45877600-45887400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:45877600-45889600	Weak transcription	Placenta	Placenta
16	chr1:45878200-45879600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:45878600-45879600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:45878600-45879600	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:45878600-45880200	Enhancers	Brain Hippocampus Middle	brain
20	chr1:45878600-45880800	Enhancers	Brain Substantia Nigra	brain
21	chr1:45878600-45881400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:45878800-45879200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:45878800-45879200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:45878800-45879600	Enhancers	Brain Anterior Caudate	brain
25	chr1:45878800-45879600	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:45878800-45880200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:45879000-45879200	Enhancers	K562	blood
28	chr1:45879000-45879800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr1:45879000-45881800	Weak transcription	Primary T cells from cord blood	blood
30	chr1:45879000-45887200	Weak transcription	Primary hematopoietic stem cells	blood

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