Variant report

Variant	rs6770452
Chromosome Location	chr3:78853165-78853166
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1033185	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923155	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1355983	0.91[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487135	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162423	0.87[CHB][hapmap];0.80[YRI][hapmap]
rs162425	0.91[CHB][hapmap]
rs162428	0.87[CHB][hapmap]
rs162429	0.87[CHB][hapmap]
rs17311036	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17311057	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17311169	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17376753	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1825760	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865861	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs2018432	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2082973	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329805	0.87[CHB][hapmap]
rs329812	0.86[CHB][hapmap]
rs329813	0.93[CHB][hapmap]
rs329819	0.87[CHB][hapmap]
rs331134	0.84[CHB][hapmap]
rs331149	0.84[CHB][hapmap]
rs331158	0.93[CHB][hapmap];0.86[CHD][hapmap];0.89[LWK][hapmap];0.81[YRI][hapmap]
rs333483	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333493	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333506	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333507	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35077320	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35556205	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681011	0.82[ASN][1000 genomes]
rs4681013	0.92[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs531125	0.86[CHB][hapmap]
rs57046576	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58611756	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58792018	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59263997	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6548595	0.86[CHB][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6548600	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496525	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66528054	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67488304	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67703869	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805432	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72892461	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72892501	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73113488	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73117115	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73848602	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610996	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617433	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629522	0.84[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638321	0.83[ASN][1000 genomes]
rs7650002	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9866912	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv432459	chr3:78819310-78874310	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78844200-78853600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:78844400-78854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:78850800-78854400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:78850800-78854400	Enhancers	Fetal Lung	lung
5	chr3:78851000-78853200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:78851000-78854600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:78851400-78853400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:78851400-78854000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:78851600-78853400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:78851600-78853600	Weak transcription	NHDF-Ad	bronchial
12	chr3:78851600-78853800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:78851600-78861200	Weak transcription	Brain Angular Gyrus	brain
14	chr3:78852200-78854200	Enhancers	Brain Hippocampus Middle	brain
15	chr3:78852400-78853200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:78852400-78853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:78852400-78853800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:78852400-78853800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:78852400-78854200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:78852600-78853600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:78852600-78853600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:78852600-78859400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:78852800-78853800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:78853000-78854200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:78853000-78854400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr3:78853000-78854800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:78853000-78855200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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