Variant report

Variant	rs4660858
Chromosome Location	chr1:45936351-45936352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45240683..45242333-chr1:45936200..45938489,2	K562	blood:
2	chr1:45934784..45936489-chr1:45953495..45956365,2	K562	blood:
3	chr1:45933683..45936591-chr1:45937552..45940709,3	K562	blood:
4	chr1:45936186..45938090-chr1:45940024..45942572,2	K562	blood:

Variant related genes	Relation type
ENSG00000142937	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000225721	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1006216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1007858	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789463	0.81[JPT][hapmap]
rs10789464	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1084166	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10890327	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890330	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211101	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211108	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211111	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211117	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211118	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211123	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211128	0.82[AMR][1000 genomes]
rs12029322	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037201	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12037411	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042903	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12046816	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049503	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap]
rs12066142	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067642	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097497	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12410493	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564806	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1417578	0.87[EUR][1000 genomes]
rs1494812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17395553	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1771551	0.95[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1826691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2050884	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs2055145	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088100	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153607	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs2153608	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs2153609	0.91[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2185549	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs2298018	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs2487442	0.87[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2492836	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2492840	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs28555082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3219463	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs3219472	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs3219489	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs34673142	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3790582	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790583	0.88[AMR][1000 genomes];0.85[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];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660301	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660849	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660851	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4660852	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660853	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs4660854	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs4660855	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660863	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55642258	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788261	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61788262	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61788281	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61788285	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788336	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61791362	0.85[EUR][1000 genomes]
rs61791368	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61791369	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6657284	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]
rs67683090	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs713358	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7417107	0.87[EUR][1000 genomes]
rs7525849	0.80[EUR][1000 genomes]
rs7528573	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532762	0.87[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7536135	0.80[EUR][1000 genomes]
rs7543428	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs7544178	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553318	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs781226	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs781230	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs781232	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs868351	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs884962	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9326141	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429072	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs9429074	0.82[EUR][1000 genomes]
rs9429076	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9429158	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs9429159	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429160	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9429161	0.87[EUR][1000 genomes]
rs9727262	0.81[EUR][1000 genomes]
rs9729395	0.84[AMR][1000 genomes];0.84[EUR][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	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
3	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
4	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
5	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
6	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
7	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
8	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
9	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4660858	SPATA19	trans	parietal	SCAN
rs4660858	Hs.396207	cis	multi-tissue	Pritchard
rs4660858	GPBP1L1	cis	Lymphoblastoid	GTEx
rs4660858	MMACHC	cis	multi-tissue	Pritchard
rs4660858	CYP4Z2P	cis	cerebellum	SCAN
rs4660858	ST3GAL3	cis	parietal	SCAN
rs4660858	CLDN19	cis	cerebellum	SCAN
rs4660858	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs4660858	MAST2	cis	cerebellum	SCAN
rs4660858	C2orf49	trans	lymphoblastoid	RTeQTL
rs4660858	TESK2	cis	Whole Blood	GTEx
rs4660858	PRDX1	cis	Thyroid	GTEx
rs4660858	IPP	cis	lymphoblastoid	seeQTL
rs4660858	MMACHC	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:45915400-45940600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:45919000-45941000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:45923400-45940600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:45923600-45951600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:45933600-45938200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:45934400-45936400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:45935200-45936600	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:45935600-45943400	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:45935800-45938800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:45936000-45936400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:45936200-45939000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:45936200-45939000	Weak transcription	Brain Substantia Nigra	brain

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