Variant report

Variant	rs2175544
Chromosome Location	chr3:145959813-145959814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145956753..145960171-chr3:145962648..145965540,3	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10737947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10804710	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935611	0.94[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10935613	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935614	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935615	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10935616	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11709096	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716310	0.93[ASN][1000 genomes]
rs11915448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11919011	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12487353	0.82[ASN][1000 genomes]
rs12633074	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1355570	0.85[EUR][1000 genomes]
rs1398125	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1398529	0.94[ASN][1000 genomes]
rs1512078	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512079	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512080	0.90[ASN][1000 genomes]
rs1512081	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512888	0.93[ASN][1000 genomes]
rs1512890	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1512893	0.91[ASN][1000 genomes]
rs1606434	0.90[ASN][1000 genomes]
rs1877511	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1913184	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs2036980	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs2175545	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867081	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867082	0.90[ASN][1000 genomes]
rs2867083	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867084	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2903478	0.93[ASN][1000 genomes]
rs2903479	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762686	0.92[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs3762688	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs3792338	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3804648	0.93[ASN][1000 genomes]
rs3804654	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3914252	0.93[ASN][1000 genomes]
rs4273339	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4475004	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4488802	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681306	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681307	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4681308	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440421	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs6440422	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6770057	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs6770163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6770278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6775520	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792732	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800307	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6805377	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7430290	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612683	0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621841	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632412	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633252	0.89[ASN][1000 genomes]
rs7634568	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643778	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645100	0.85[EUR][1000 genomes]
rs907490	0.84[EUR][1000 genomes]
rs9756128	0.93[ASN][1000 genomes]
rs9809892	0.93[ASN][1000 genomes]
rs9813122	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822280	0.93[ASN][1000 genomes]
rs9825776	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826132	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826360	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9826591	0.90[ASN][1000 genomes]
rs9830892	0.90[ASN][1000 genomes]
rs9836419	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs9838801	0.94[ASN][1000 genomes]
rs9838866	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9839724	0.93[ASN][1000 genomes]
rs9839874	0.92[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs9845890	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850566	0.93[ASN][1000 genomes]
rs9851511	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855695	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9858823	0.90[ASN][1000 genomes]
rs9859273	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs9863647	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867851	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9873891	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9875799	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9877004	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877614	chr3:145903426-146025896	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv877615	chr3:145910430-145988231	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv877616	chr3:145921954-145983688	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3333601	chr3:145940702-146068210	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3416330	chr3:145941029-146068457	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3452197	chr3:145950303-145974111	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3333990	chr3:145950303-145982133	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145948000-145967800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145953200-145968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:145954600-145962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:145954600-145967800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:145955200-145962400	Weak transcription	Fetal Lung	lung
6	chr3:145956200-145960200	Weak transcription	NHDF-Ad	bronchial
7	chr3:145956200-145964600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:145956800-145966600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:145958000-145965400	Weak transcription	Adipose Nuclei	Adipose
10	chr3:145958000-145966000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:145959400-145960000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:145959400-145960200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:145959400-145962800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:145959400-145966400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:145959600-145960400	Enhancers	HUVEC	blood vessel
16	chr3:145959800-145960000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr3:145959800-145960000	Enhancers	Ovary	ovary
18	chr3:145959800-145960200	Flanking Active TSS	Osteobl	bone
19	chr3:145959800-145960400	ZNF genes & repeats	Fetal Stomach	stomach

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