Variant report

Variant	rs6782997
Chromosome Location	chr3:51410517-51410518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13316894	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13317936	1.00[AMR][1000 genomes]
rs13321111	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322621	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13353505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051799	1.00[MEX][hapmap]
rs28454463	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28890042	1.00[AMR][1000 genomes]
rs6777506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6779163	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6806124	1.00[AMR][1000 genomes]
rs7627636	1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]
rs7635546	1.00[AMR][1000 genomes]
rs9812682	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9826415	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9826735	0.82[YRI][hapmap]
rs9828325	1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs9829002	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841963	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9846343	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853900	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9855214	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9868612	1.00[AMR][1000 genomes]
rs9875513	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9878053	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9880909	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv460534	chr3:51393046-51416108	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv590274	chr3:51393046-51416108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv460535	chr3:51395571-51416108	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv590275	chr3:51395571-51416108	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
3	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
4	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
5	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:51400600-51411400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:51400800-51410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:51400800-51411000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:51400800-51411400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:51400800-51411400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:51400800-51412200	Weak transcription	HSMMtube	muscle
12	chr3:51401000-51411800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:51406000-51411200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:51406000-51411600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:51406000-51417000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:51406000-51420200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:51406000-51420400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:51406000-51420400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:51406000-51420600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:51406000-51420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:51406000-51420800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:51406000-51421400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:51406400-51411800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:51406400-51420600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:51406400-51421600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:51408200-51411200	Weak transcription	Fetal Brain Female	brain
27	chr3:51408800-51411000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:51409000-51410800	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:51409200-51410800	Weak transcription	Brain Angular Gyrus	brain
30	chr3:51409800-51411200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:51410000-51421400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:51410400-51411200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:51410400-51417800	Strong transcription	Brain Germinal Matrix	brain
34	chr3:51410400-51420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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