Variant report

Variant	rs4771835
Chromosome Location	chr13:92138595-92138596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:92135261..92136861-chr13:92137594..92139978,2	K562	blood:
2	chr13:92115826..92117568-chr13:92136688..92139135,2	K562	blood:
3	chr13:92135361..92137135-chr13:92138478..92140147,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPC6-6	chr13:92138065-92139124	NONHSAT034696

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1316585	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2147191	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3848055	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3903848	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs4620821	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap]
rs4771836	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs481729	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs496952	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497795	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs499769	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs505889	0.84[ASN][1000 genomes]
rs559914	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs576149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs582961	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs612573	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs618839	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647716	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492547	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650365	0.94[ASN][1000 genomes]
rs653774	0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs655169	0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs659897	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs679631	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681903	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7320241	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7987869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556091	0.84[ASN][1000 genomes]
rs9556095	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9556097	0.92[ASN][1000 genomes]
rs9556098	0.93[ASN][1000 genomes]
rs9560807	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs9560808	0.82[ASN][1000 genomes]
rs9560814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9560815	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9560820	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9560821	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv1049382	chr13:92024240-92521180	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv541873	chr13:92024240-92521180	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv562714	chr13:92056911-92304974	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1036860	chr13:92061347-92291771	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv562715	chr13:92061878-92299609	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1041168	chr13:92062057-92301861	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv949582	chr13:92062331-92301861	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1041762	chr13:92065459-92267509	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv541874	chr13:92065459-92267509	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv529091	chr13:92065460-92267510	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1045465	chr13:92065659-92267370	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv541875	chr13:92065659-92267370	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv531890	chr13:92065660-92267369	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1040707	chr13:92072034-92302281	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1045421	chr13:92075673-92283600	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv541876	chr13:92075673-92283600	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1044789	chr13:92083774-92209971	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv541877	chr13:92083774-92209971	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv530635	chr13:92084151-92280466	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1045669	chr13:92111663-92245308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv541878	chr13:92111663-92245308	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv562716	chr13:92128694-92250454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	nsv562717	chr13:92135345-92250454	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv514714	chr13:92138511-92142319	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92133800-92157000	Weak transcription	Hela-S3	cervix
2	chr13:92138000-92139200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:92138000-92139400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:92138000-92139600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:92138400-92139200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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