Variant report

Variant	rs2959051
Chromosome Location	chr15:31255707-31255708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31252830..31256274-chr15:31263661..31267030,3	K562	blood:
2	chr15:31253352..31256135-chr15:31282312..31285268,3	K562	blood:
3	chr15:31253352..31256135-chr15:31282609..31285268,3	K562	blood:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12437580	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12443369	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12906480	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12914207	0.81[ASN][1000 genomes]
rs1404467	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2140735	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2272218	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2272219	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293319	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2293320	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2339048	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2949572	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2949575	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2949576	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2949578	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955787	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2955791	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959047	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959050	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743231	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71474640	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164530	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170772	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175256	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175951	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183880	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041717	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
10	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2959051	RP11-932O9.7	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31225400-31255800	Strong transcription	Fetal Intestine Large	intestine
2	chr15:31225800-31256000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:31226000-31255800	Strong transcription	Fetal Stomach	stomach
4	chr15:31226000-31258800	Strong transcription	Duodenum Mucosa	Duodenum
5	chr15:31226200-31269200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:31226400-31260800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:31227000-31269600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:31227200-31255800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:31227200-31258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:31228600-31258800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr15:31229200-31261000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:31230400-31258800	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:31233400-31269200	Strong transcription	Liver	Liver
14	chr15:31237200-31269600	Strong transcription	Primary B cells from cord blood	blood
15	chr15:31242000-31282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:31242400-31255800	Strong transcription	Fetal Intestine Small	intestine
17	chr15:31243200-31267600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:31245000-31276400	Weak transcription	Brain Germinal Matrix	brain
19	chr15:31247000-31270200	Weak transcription	K562	blood
20	chr15:31247400-31260600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:31247600-31261000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:31247800-31258800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr15:31248800-31259800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:31248800-31283000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:31249000-31269600	Strong transcription	HUVEC	blood vessel
26	chr15:31249000-31270200	Weak transcription	Stomach Mucosa	stomach
27	chr15:31249000-31276000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:31250200-31282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:31250800-31257800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:31250800-31257800	Weak transcription	NHDF-Ad	bronchial
31	chr15:31250800-31261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:31250800-31270600	Weak transcription	Small Intestine	intestine
33	chr15:31250800-31282400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:31251200-31258000	Weak transcription	NHLF	lung
35	chr15:31251200-31272400	Weak transcription	Aorta	Aorta
36	chr15:31251200-31277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:31251200-31282400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:31251400-31256200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:31251400-31257200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:31251400-31257800	Weak transcription	Gastric	stomach
41	chr15:31251400-31258000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:31251400-31265800	Weak transcription	A549	lung
43	chr15:31251600-31282200	Weak transcription	Hela-S3	cervix
44	chr15:31252000-31256000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:31252000-31257000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:31252000-31272200	Weak transcription	Spleen	Spleen
47	chr15:31252600-31258000	Weak transcription	Lung	lung
48	chr15:31252800-31257200	Weak transcription	NH-A	brain
49	chr15:31252800-31257600	Weak transcription	HSMM	muscle
50	chr15:31252800-31257800	Weak transcription	Colon Smooth Muscle	Colon

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