Variant report

Variant	rs12437955
Chromosome Location	chr15:58984407-58984408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58982751..58984795-chr15:59030172..59031707,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLTM-6	chr15:58982672-58985806	NR_073415

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11071393	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11853494	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11856657	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12437998	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438487	0.84[AMR][1000 genomes]
rs12440091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440267	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441313	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12441912	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12442451	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12442956	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591291	0.81[AMR][1000 genomes]
rs12591543	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12592332	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12708455	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12905110	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12905173	0.84[AMR][1000 genomes]
rs12906705	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12908261	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908449	0.81[ASN][1000 genomes]
rs12910927	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12912286	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12912327	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12915950	0.86[AMR][1000 genomes]
rs12916010	0.86[AMR][1000 genomes]
rs16940589	0.88[AMR][1000 genomes]
rs16940647	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17301905	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17301954	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1820548	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2052804	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052805	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303532	0.86[AMR][1000 genomes]
rs28417700	0.84[AMR][1000 genomes]
rs28455654	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28457680	0.89[AMR][1000 genomes]
rs28489732	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28542491	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28549001	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28576281	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584993	0.88[AMR][1000 genomes]
rs28600144	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28609304	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28637832	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28639679	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28678478	0.81[ASN][1000 genomes]
rs28724298	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28734088	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs28818840	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28852159	0.84[AMR][1000 genomes]
rs35499736	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35956992	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs544282	0.85[ASN][1000 genomes]
rs6494030	0.88[AMR][1000 genomes]
rs6494031	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6494032	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6494033	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6494034	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6494038	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163733	0.80[ASN][1000 genomes]
rs7163939	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7164620	0.89[AMR][1000 genomes]
rs7165035	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7167528	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7170314	0.84[AMR][1000 genomes]
rs7174414	0.80[ASN][1000 genomes]
rs7180550	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8026668	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029805	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8033565	0.84[AMR][1000 genomes]
rs8033691	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035960	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036005	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8036448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8039791	0.86[AMR][1000 genomes]
rs8040358	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9302203	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9744518	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9920042	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9920310	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9920720	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9921024	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv974583	chr15:58979010-58987450	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:58936200-58991400	Weak transcription	HMEC	breast
3	chr15:58951200-58987000	Weak transcription	NHEK	skin
4	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:58961800-58984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
14	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
15	chr15:58970600-58987200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:58971800-58984800	Weak transcription	NHDF-Ad	bronchial
17	chr15:58971800-58986800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:58972000-58986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:58972600-58988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:58972600-58988800	Weak transcription	Fetal Stomach	stomach
21	chr15:58972600-58989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:58973200-58984600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr15:58973200-58984800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:58974600-58991000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:58975800-58989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:58976800-58986400	Weak transcription	Gastric	stomach
27	chr15:58976800-58986600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:58977000-58984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:58977000-58988600	Weak transcription	Fetal Intestine Small	intestine
30	chr15:58977000-58989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:58977200-58984800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:58977200-58984800	Weak transcription	Hela-S3	cervix
33	chr15:58977200-58986600	Weak transcription	Stomach Mucosa	stomach
34	chr15:58977200-58986800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:58977200-58989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:58977200-58989200	Weak transcription	Pancreas	Pancrea
37	chr15:58977200-58989400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:58977200-58996400	Weak transcription	NHLF	lung
39	chr15:58977200-58998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:58977200-59004400	Weak transcription	Ovary	ovary
41	chr15:58977200-59007800	Weak transcription	HepG2	liver
42	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:58978600-58986400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:58978800-58989200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:58979200-58986400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:58980400-58989800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:58982400-58984600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:58982400-58991400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:58982600-58990000	Weak transcription	Primary hematopoietic stem cells	blood

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