Variant report

Variant	rs2960354
Chromosome Location	chr19:39018280-39018281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39015980..39018585-chr19:39108348..39111291,2	K562	blood:

Variant related genes	Relation type
ENSG00000104814	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10469270	0.89[EUR][1000 genomes]
rs12327672	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2116869	0.88[EUR][1000 genomes]
rs2228071	0.90[EUR][1000 genomes]
rs2229145	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2229147	1.00[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2234709	0.90[EUR][1000 genomes]
rs2459631	0.93[ASW][hapmap];0.84[YRI][hapmap]
rs2960320	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2960350	0.82[ASW][hapmap]
rs35959206	0.87[EUR][1000 genomes]
rs45555835	0.98[EUR][1000 genomes]
rs61361030	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73544610	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73544616	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs892052	0.88[YRI][hapmap]
rs908644	0.92[YRI][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
4	chr19:38997600-39025400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:38998600-39025000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:39001000-39025600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:39005800-39025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:39006200-39025400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:39006800-39025600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:39007000-39020400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr19:39007000-39025600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:39007600-39025000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:39007600-39025200	Weak transcription	Brain Hippocampus Middle	brain
14	chr19:39007800-39025400	Weak transcription	Brain Anterior Caudate	brain
15	chr19:39008000-39021800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:39008600-39021800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:39008600-39025200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:39009000-39021800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:39010200-39018600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:39014200-39022000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:39016800-39019200	Enhancers	Brain Germinal Matrix	brain
22	chr19:39016800-39019800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:39017800-39021000	Weak transcription	HSMMtube	muscle
24	chr19:39018200-39019200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr19:39018200-39019400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:39018200-39019400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links