Variant report

Variant	rs7543428
Chromosome Location	chr1:45839643-45839644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45804454..45807409-chr1:45839632..45842085,2	MCF-7	breast:
2	chr1:45807846..45810549-chr1:45838820..45841391,2	K562	blood:
3	chr1:45837055..45840025-chr1:45851538..45853151,2	K562	blood:

Variant related genes	Relation type
ENSG00000132773	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1006216	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs1007858	0.86[EUR][1000 genomes]
rs1084166	0.86[EUR][1000 genomes]
rs10890327	0.89[EUR][1000 genomes]
rs10890330	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs11211101	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211108	0.90[EUR][1000 genomes]
rs11211111	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs11211117	0.87[EUR][1000 genomes]
rs11211118	0.87[EUR][1000 genomes]
rs11211124	0.82[CHD][hapmap]
rs12029322	0.82[CHD][hapmap]
rs12037201	0.86[EUR][1000 genomes]
rs12037411	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12046816	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs12067642	0.81[EUR][1000 genomes]
rs12097497	0.90[EUR][1000 genomes]
rs12410493	0.89[EUR][1000 genomes]
rs12564806	0.80[EUR][1000 genomes]
rs1417578	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs1538969	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1538970	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17395553	0.96[EUR][1000 genomes]
rs1771551	0.86[CEU][hapmap];0.91[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1826691	0.91[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs2050884	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055145	0.86[CEU][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs2088100	0.90[EUR][1000 genomes]
rs2153607	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153609	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2185549	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];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2298018	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2487442	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2492836	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28555082	0.87[EUR][1000 genomes]
rs3219463	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3219472	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219489	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3790582	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.89[EUR][1000 genomes]
rs4520450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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]
rs4660301	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660849	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];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660852	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4660854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660855	0.89[EUR][1000 genomes]
rs4660858	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.87[EUR][1000 genomes]
rs4660863	0.82[CHD][hapmap]
rs55642258	0.81[EUR][1000 genomes]
rs61788261	0.89[EUR][1000 genomes]
rs61788262	0.84[EUR][1000 genomes]
rs61788281	0.87[EUR][1000 genomes]
rs61788285	0.81[EUR][1000 genomes]
rs61791362	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61791368	0.88[EUR][1000 genomes]
rs61791369	0.91[EUR][1000 genomes]
rs6657284	0.91[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap]
rs6670303	0.83[EUR][1000 genomes]
rs72686460	0.86[EUR][1000 genomes]
rs7417107	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7525849	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7528573	0.87[EUR][1000 genomes]
rs7531253	0.91[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes]
rs7532762	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536135	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544178	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553318	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781226	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs781230	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs781232	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs884962	0.95[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429073	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9429074	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9429076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9429158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9429159	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9429160	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]
rs9429161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7543428	IPP	cis	lymphoblastoid	seeQTL
rs7543428	CLDN19	cis	cerebellum	SCAN
rs7543428	GPBP1L1	cis	Lymphoblastoid	GTEx
rs7543428	MAST2	cis	cerebellum	SCAN
rs7543428	MUTYH	cis	multi-tissue	Pritchard
rs7543428	MMACHC	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45826200-45867200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:45827000-45859000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:45827200-45842000	Weak transcription	Right Atrium	heart
4	chr1:45834200-45841200	Weak transcription	Aorta	Aorta
5	chr1:45837200-45849800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:45837600-45840600	Weak transcription	Small Intestine	intestine
7	chr1:45839200-45840000	Enhancers	Brain Hippocampus Middle	brain
8	chr1:45839200-45840000	Enhancers	Brain Substantia Nigra	brain
9	chr1:45839200-45840000	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:45839200-45840000	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:45839200-45840400	Enhancers	Primary B cells from cord blood	blood
12	chr1:45839400-45839800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:45839400-45839800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:45839400-45839800	Enhancers	Fetal Intestine Large	intestine
15	chr1:45839400-45839800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:45839400-45840000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:45839400-45840000	Enhancers	Colon Smooth Muscle	Colon
18	chr1:45839400-45840000	Enhancers	Fetal Heart	heart
19	chr1:45839400-45840000	Enhancers	Psoas Muscle	Psoas
20	chr1:45839400-45840200	Enhancers	Liver	Liver
21	chr1:45839400-45841200	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:45839400-45842400	Enhancers	Ovary	ovary
23	chr1:45839600-45839800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:45839600-45840800	Weak transcription	Fetal Lung	lung
25	chr1:45839600-45841000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:45839600-45841600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:45839600-45850600	Weak transcription	Monocytes-CD14+_RO01746	blood

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