Variant report

Variant	rs10451867
Chromosome Location	chr3:142790604-142790605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142782763..142785207-chr3:142789429..142791710,3	K562	blood:
2	chr3:142716811..142718483-chr3:142789179..142792100,2	K562	blood:
3	chr3:142790255..142790841-chr3:143363451..143364029,2	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10413	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1043898	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10513184	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053950	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10790	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10935475	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs10935479	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11709036	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11915462	0.90[EUR][1000 genomes]
rs11922201	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12485790	0.82[EUR][1000 genomes]
rs12490776	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492904	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs12695770	0.83[EUR][1000 genomes]
rs13075955	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088422	0.83[EUR][1000 genomes]
rs13094293	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13099995	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1349262	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs13715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375814	0.91[EUR][1000 genomes]
rs1449868	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1449869	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs1530753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs1532588	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs1545597	0.83[EUR][1000 genomes]
rs17557029	0.89[EUR][1000 genomes]
rs1814565	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1827159	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs1839406	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs1868569	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1868570	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1965343	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs2045306	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124541	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs2124542	0.88[EUR][1000 genomes]
rs2124543	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[EUR][1000 genomes]
rs2137586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2175739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290549	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs2353408	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353409	0.95[EUR][1000 genomes]
rs2353411	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs3821645	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs3856697	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3902877	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[EUR][1000 genomes]
rs4030582	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs4683444	0.94[EUR][1000 genomes]
rs4683721	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683722	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4683723	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683724	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56382522	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440129	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs6440131	0.94[EUR][1000 genomes]
rs6440132	0.92[EUR][1000 genomes]
rs6440133	0.87[EUR][1000 genomes]
rs6440134	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770102	0.88[EUR][1000 genomes]
rs6778454	0.88[EUR][1000 genomes]
rs6781080	0.92[EUR][1000 genomes]
rs6781887	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs6783145	0.92[EUR][1000 genomes]
rs6784200	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6796771	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6805417	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs6806551	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808406	0.81[EUR][1000 genomes]
rs6808689	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs7611721	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs7623532	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644475	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648143	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649225	0.92[EUR][1000 genomes]
rs7652745	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs766360	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs936194	0.95[EUR][1000 genomes]
rs936196	0.93[EUR][1000 genomes]
rs936197	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937498	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814656	0.92[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816317	0.95[EUR][1000 genomes]
rs9820175	0.81[EUR][1000 genomes]
rs9831162	0.82[EUR][1000 genomes]
rs9835348	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs9847059	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9851353	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862433	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875210	0.82[EUR][1000 genomes]
rs9877128	0.95[EUR][1000 genomes]
rs9877135	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1004467	chr3:142768867-142800605	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1004682	chr3:142768867-142804154	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10451867	SLC9A9	cis	parietal	SCAN
rs10451867	CHST2	cis	parietal	SCAN
rs10451867	U2SURP	cis	lymphoblastoid	seeQTL
rs10451867	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142765400-142791600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:142775600-142794400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:142788600-142790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:142789200-142790800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:142789200-142791000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:142789400-142790800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:142789400-142790800	Enhancers	HSMM	muscle
8	chr3:142789400-142791000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:142789400-142791000	Enhancers	HMEC	breast
10	chr3:142789400-142791000	Enhancers	HSMMtube	muscle
11	chr3:142789400-142791200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:142789600-142790800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:142789600-142790800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:142789600-142791000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:142789600-142791000	Enhancers	Duodenum Mucosa	Duodenum
16	chr3:142789600-142791200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:142789600-142791600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:142789600-142791800	Enhancers	NHEK	skin
19	chr3:142789800-142790800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:142789800-142790800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:142789800-142791000	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:142789800-142794000	Enhancers	K562	blood
23	chr3:142790000-142791200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:142790000-142791200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr3:142790000-142791800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:142790200-142790800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:142790200-142791000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:142790200-142792600	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr3:142790400-142790800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr3:142790400-142791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:142790600-142790800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:142790600-142790800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:142790600-142790800	Enhancers	Osteobl	bone
34	chr3:142790600-142791600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:142790600-142792000	Weak transcription	Fetal Intestine Small	intestine

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