Variant report

Variant	rs36034566
Chromosome Location	chr17:19911649-19911650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:19911508-19914638	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912985-19912998 chr17:19912998-19913011 chr17:19912617-19912633 chr17:19912019-19912028 chr17:19912619-19912629 chr17:19912616-19912634
2	TCF12	chr17:19911526-19914125	A549	lung:	n/a	n/a
3	ZNF263	chr17:19911453-19914279	HEK293-T-REx	kidney:	n/a	chr17:19913782-19913791 chr17:19913411-19913420 chr17:19913012-19913021 chr17:19913789-19913798
4	MAX	chr17:19911533-19914165	A549	lung:	n/a	chr17:19912536-19912546

No.	Distal block	Cell Line	Cell type
1	chr17:19770311..19771954-chr17:19910328..19912594,2	MCF-7	breast:
2	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
3	chr17:19879669..19882225-chr17:19910498..19912176,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKAP10-1	chr17:19911364-19912547	ENSG00000261033.1
2	lnc-AKAP10-1	chr17:19911368-19912547	NONHSAT146538

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000083290	Chromatin interaction
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1034904	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1860302	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2108979	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2108980	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34291370	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3909258	0.80[EUR][1000 genomes]
rs4479308	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924801	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4925065	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925066	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4925067	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56142708	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7211535	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7215514	0.88[EUR][1000 genomes]
rs7218708	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9891739	0.80[EUR][1000 genomes]
rs9906625	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9909009	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19911400-19911800	Enhancers	K562	blood
2	chr17:19911400-19912000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr17:19911400-19912000	Bivalent Enhancer	Primary T cells from cord blood	blood
4	chr17:19911400-19912200	Flanking Active TSS	A549	lung
5	chr17:19911600-19911800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr17:19911600-19911800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:19911600-19911800	Enhancers	H9 Cell Line	embryonic stem cell
8	chr17:19911600-19911800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
9	chr17:19911600-19911800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:19911600-19911800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:19911600-19911800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr17:19911600-19911800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:19911600-19911800	Enhancers	Brain Cingulate Gyrus	brain
14	chr17:19911600-19911800	Enhancers	Brain Hippocampus Middle	brain
15	chr17:19911600-19911800	Active TSS	Hela-S3	cervix
16	chr17:19911600-19911800	Bivalent Enhancer	HepG2	liver
17	chr17:19911600-19911800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr17:19911600-19912000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr17:19911600-19912000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:19911600-19912000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:19911600-19913600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr17:19911600-19913800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links