Variant report

Variant	rs9429160
Chromosome Location	chr1:45827968-45827969
allele	G/T
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	KAP1	chr1:45827811-45828520	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45826987..45828662-chr1:45989193..45991039,2	K562	blood:
2	chr1:45804195..45807360-chr1:45826086..45829003,3	K562	blood:
3	chr1:45827704..45830236-chr1:45833381..45835758,2	K562	blood:

Variant related genes	Relation type
ENSG00000238945	TF binding region
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1006216	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1007858	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1084166	0.83[EUR][1000 genomes]
rs10890327	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10890330	0.86[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11211101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211108	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211111	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211117	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211118	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12029322	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12037201	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12037411	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046816	0.90[CEU][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12067642	0.85[ASN][1000 genomes]
rs12097497	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12410493	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1417578	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1538969	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1538970	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17395553	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771551	0.86[CEU][hapmap];0.80[GIH][hapmap];0.87[EUR][1000 genomes]
rs1826691	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050884	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2055145	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2088100	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2153607	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2153608	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2153609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2185549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298018	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2487442	0.95[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs2492836	0.84[EUR][1000 genomes]
rs2492840	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28555082	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3219463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3219472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3219489	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3790582	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520450	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4633317	0.82[CHB][hapmap]
rs4660301	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660851	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660852	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4660854	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4660855	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4660858	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]
rs4660863	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs55642258	0.85[ASN][1000 genomes]
rs61788261	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61788262	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788281	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61788285	0.85[ASN][1000 genomes]
rs61791362	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61791368	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61791369	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657284	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6670303	0.81[EUR][1000 genomes]
rs713358	0.82[CHB][hapmap]
rs72686460	0.85[EUR][1000 genomes]
rs7417107	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7525849	0.87[EUR][1000 genomes]
rs7528573	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7531253	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532762	0.95[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs7536135	0.87[EUR][1000 genomes]
rs7543428	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7553318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs781226	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[EUR][1000 genomes]
rs781230	0.87[EUR][1000 genomes]
rs781232	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.87[EUR][1000 genomes]
rs868351	0.82[CHB][hapmap]
rs884962	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429072	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9429073	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9429074	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9429076	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9429158	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9429159	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9429161	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9429160	MMACHC	cis	multi-tissue	Pritchard
rs9429160	IPP	cis	lymphoblastoid	seeQTL
rs9429160	MAST2	cis	cerebellum	SCAN
rs9429160	GPBP1L1	cis	Lymphoblastoid	GTEx
rs9429160	ST3GAL3	cis	parietal	SCAN
rs9429160	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs9429160	Hs.396207	cis	multi-tissue	Pritchard
rs9429160	CLDN19	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45812800-45835800	Weak transcription	Thymus	Thymus
2	chr1:45825600-45828000	Enhancers	Brain Hippocampus Middle	brain
3	chr1:45825600-45828000	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:45825800-45828000	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:45825800-45828000	Enhancers	Brain Substantia Nigra	brain
6	chr1:45826200-45836200	Weak transcription	Primary B cells from cord blood	blood
7	chr1:45826200-45867200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:45827000-45829800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:45827000-45830600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:45827000-45830800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:45827000-45836000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:45827000-45859000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:45827200-45830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:45827200-45842000	Weak transcription	Right Atrium	heart
15	chr1:45827400-45830400	Weak transcription	GM12878-XiMat	blood
16	chr1:45827600-45830200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:45827600-45830800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:45827600-45839400	Weak transcription	Liver	Liver

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