Variant report

Variant	rs2960317
Chromosome Location	chr19:39036011-39036012
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39035426..39037334-chr19:39139289..39140832,2	K562	blood:
2	chr19:39033172..39036412-chr19:39037332..39039835,4	K562	blood:
3	chr19:39034364..39037284-chr19:39108616..39110630,2	K562	blood:
4	chr19:39033262..39037138-chr19:39114289..39118400,4	K562	blood:
5	chr19:39033816..39036300-chr19:39320862..39322529,2	MCF-7	breast:
6	chr19:38951538..38953611-chr19:39035456..39038099,2	K562	blood:
7	chr19:39033355..39037027-chr19:39040774..39043679,3	K562	blood:
8	chr19:39033772..39036275-chr19:39124908..39126988,2	MCF-7	breast:
9	chr19:39034798..39036647-chr19:39056584..39059105,2	MCF-7	breast:
10	chr19:39033295..39037284-chr19:39108058..39111883,5	K562	blood:
11	chr19:39033468..39036345-chr19:39125493..39127888,3	K562	blood:
12	chr19:39033844..39036603-chr19:39138294..39139887,2	K562	blood:
13	chr19:39033384..39036751-chr19:39123967..39127917,4	K562	blood:
14	chr19:39015321..39017882-chr19:39033262..39036182,2	K562	blood:
15	chr19:38997702..38999561-chr19:39033477..39036015,2	MCF-7	breast:
16	chr19:39014964..39016821-chr19:39033783..39036182,2	K562	blood:
17	chr19:39035080..39036958-chr19:39218564..39220441,2	K562	blood:
18	chr19:39034770..39036349-chr19:39131227..39134089,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000196218	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12974674	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12981340	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1568191	0.83[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2071091	0.91[AFR][1000 genomes]
rs2254484	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2915945	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2945048	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960318	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2960321	0.83[ASW][hapmap]
rs2960322	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786829	0.89[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4802603	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249859	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1058902	chr19:39025940-39078574	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1064490	chr19:39029788-39078574	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2960317	SAE1	cis	parietal	SCAN
rs2960317	PAF1	cis	parietal	SCAN
rs2960317	CLPTM1	cis	cerebellum	SCAN
rs2960317	CAPN12	cis	lymphoblastoid	seeQTL
rs2960317	USP13	trans	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
2	chr19:39026000-39052400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39029000-39051600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:39029600-39046000	Weak transcription	HSMM	muscle
5	chr19:39030000-39054600	Strong transcription	Fetal Muscle Leg	muscle
6	chr19:39030200-39055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr19:39033600-39036600	Strong transcription	HSMMtube	muscle
8	chr19:39034200-39036200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:39034600-39036200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:39034600-39051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39035000-39039400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39035200-39036200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr19:39035200-39036400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:39035200-39036800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr19:39035200-39038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:39035200-39039000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:39035200-39042400	Weak transcription	Spleen	Spleen
18	chr19:39035200-39052600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:39035200-39066400	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:39035400-39036600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:39035400-39036800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:39035400-39036800	Enhancers	Adipose Nuclei	Adipose
23	chr19:39035400-39038800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:39035600-39036200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr19:39035600-39036200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:39035600-39036200	Enhancers	NHEK	skin
27	chr19:39035600-39036600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr19:39035600-39036800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39035600-39038000	Weak transcription	Primary B cells from cord blood	blood
30	chr19:39035600-39050800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:39035600-39051800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:39035600-39052000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr19:39035600-39052000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:39035600-39052000	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:39035800-39036600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:39035800-39036800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:39035800-39037800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:39035800-39038800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:39035800-39041400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:39035800-39041800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:39035800-39044600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:39035800-39044600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr19:39035800-39045000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:39035800-39047400	Weak transcription	A549	lung
45	chr19:39035800-39051800	Weak transcription	Brain Anterior Caudate	brain
46	chr19:39036000-39036400	Weak transcription	Osteobl	bone
47	chr19:39036000-39037200	Enhancers	K562	blood
48	chr19:39036000-39038000	Weak transcription	GM12878-XiMat	blood
49	chr19:39036000-39038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:39036000-39041000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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