Variant report

Variant	rs4774310
Chromosome Location	chr15:58985164-58985165
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11854073	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12439457	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12911832	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911961	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912003	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1427281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1648532	0.90[CHB][hapmap]
rs17269397	0.83[CHB][hapmap]
rs1834747	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2250583	0.81[AMR][1000 genomes]
rs2555356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28864995	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs347115	1.00[CHB][hapmap]
rs347117	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs383902	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs442495	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs474875	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs4775087	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4775094	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs507801	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs593742	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs605928	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs610877	1.00[CHB][hapmap]
rs6494035	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494037	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs653765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs673813	1.00[CHB][hapmap]
rs714696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7161889	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7163162	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7183336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs972801	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[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:111 , 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	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
12	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
13	chr15:58970600-58987200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:58971800-58986800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:58972000-58986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:58972600-58988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:58972600-58988800	Weak transcription	Fetal Stomach	stomach
18	chr15:58972600-58989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:58974600-58991000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:58975800-58989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:58976800-58986400	Weak transcription	Gastric	stomach
22	chr15:58976800-58986600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:58977000-58988600	Weak transcription	Fetal Intestine Small	intestine
24	chr15:58977000-58989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:58977200-58986600	Weak transcription	Stomach Mucosa	stomach
26	chr15:58977200-58986800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:58977200-58989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:58977200-58989200	Weak transcription	Pancreas	Pancrea
29	chr15:58977200-58989400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:58977200-58996400	Weak transcription	NHLF	lung
31	chr15:58977200-58998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:58977200-59004400	Weak transcription	Ovary	ovary
33	chr15:58977200-59007800	Weak transcription	HepG2	liver
34	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:58978600-58986400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:58978800-58989200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:58979200-58986400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:58980400-58989800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:58982400-58991400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr15:58982600-58990000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
43	chr15:58982800-58985400	Strong transcription	HSMM	muscle
44	chr15:58982800-58985600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:58983000-58989800	Weak transcription	Fetal Brain Female	brain
46	chr15:58983200-58985200	Genic enhancers	Left Ventricle	heart
47	chr15:58983200-58985200	Strong transcription	HSMMtube	muscle
48	chr15:58983200-58985400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr15:58983200-58986200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:58983200-58986400	Weak transcription	Brain Anterior Caudate	brain

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