Variant report

Variant	rs16977392
Chromosome Location	chr15:57598817-57598818
allele	A/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:9)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:57598101..57599763-chr15:57616490..57618411,2	K562	blood:
2	chr15:57598783..57599377-chr15:57608651..57609348,2	K562	blood:
3	chr15:56782970..56783589-chr15:57598753..57599463,2	MCF-7	breast:
4	chr15:57597621..57600563-chr15:57604167..57606534,3	K562	blood:
5	chr15:56787707..56790107-chr15:57597582..57600140,2	MCF-7	breast:
6	chr15:57596677..57601983-chr15:57611239..57618411,9	K562	blood:
7	chr15:57597689..57601400-chr15:57611239..57614125,3	K562	blood:
8	chr15:57438317..57439358-chr15:57598387..57599123,3	K562	blood:
9	chr15:56788444..56789415-chr15:57598413..57599206,3	K562	blood:

(count:10 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-1	chr15:57596923-57598820	ENSG00000247982
2	lnc-TCF12-1	chr15:57598616-57599266	ENSG00000247982
3	lnc-TCF12-1	chr15:57597517-57599266	ENSG00000247982
4	lnc-TCF12-1	chr15:57597517-57599266	XLOC_011264
5	lnc-TCF12-1	chr15:57595100-57599266	XLOC_011264
6	lnc-TCF12-1	chr15:57595100-57599967	XLOC_011264
7	lnc-TCF12-1	chr15:57595298-57599266	XLOC_011264
8	lnc-TCF12-1	chr15:57597517-57599266	XLOC_011264
9	lnc-TCF12-1	chr15:57597517-57599266	NONHSAT044062
10	lnc-TCF12-1	chr15:57598797-57599268	NONHSAT044059

No data

Variant related genes	Relation type
ENSG00000260172	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10518903	1.00[AMR][1000 genomes]
rs12101548	1.00[AMR][1000 genomes]
rs12102210	1.00[AMR][1000 genomes]
rs1350906	1.00[AMR][1000 genomes]
rs1381557	1.00[AMR][1000 genomes]
rs1462155	1.00[AMR][1000 genomes]
rs16977249	1.00[AMR][1000 genomes]
rs16977287	1.00[AMR][1000 genomes]
rs16977313	1.00[AMR][1000 genomes]
rs16977318	1.00[AMR][1000 genomes]
rs16977342	1.00[AMR][1000 genomes]
rs16977346	1.00[AMR][1000 genomes]
rs16977350	1.00[AMR][1000 genomes]
rs16977357	1.00[AMR][1000 genomes]
rs16977361	1.00[AMR][1000 genomes]
rs16977394	1.00[AMR][1000 genomes]
rs2011721	1.00[AMR][1000 genomes]
rs2126399	1.00[AMR][1000 genomes]
rs2248255	1.00[AMR][1000 genomes]
rs2591072	1.00[AMR][1000 genomes]
rs2591074	1.00[AMR][1000 genomes]
rs2615216	1.00[AMR][1000 genomes]
rs2615232	1.00[AMR][1000 genomes]
rs2733302	1.00[AMR][1000 genomes]
rs28404473	1.00[AMR][1000 genomes]
rs28495648	1.00[AMR][1000 genomes]
rs59762811	1.00[AMR][1000 genomes]
rs60129657	1.00[AMR][1000 genomes]
rs8031933	1.00[AMR][1000 genomes]
rs8037049	1.00[AMR][1000 genomes]
rs8039780	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57593800-57599200	Weak transcription	Small Intestine	intestine
2	chr15:57593800-57599400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
3	chr15:57598000-57599000	Flanking Active TSS	Fetal Lung	lung
4	chr15:57598000-57599200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:57598000-57599200	Active TSS	Rectal Smooth Muscle	rectum
6	chr15:57598000-57599600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr15:57598000-57599600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr15:57598200-57599000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:57598200-57599000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr15:57598200-57599000	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr15:57598200-57599200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr15:57598200-57599200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:57598200-57599200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:57598200-57599200	Active TSS	Brain Angular Gyrus	brain
15	chr15:57598200-57599200	Active TSS	Brain Hippocampus Middle	brain
16	chr15:57598200-57599200	Active TSS	Brain Substantia Nigra	brain
17	chr15:57598200-57599200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr15:57598200-57599200	Active TSS	Gastric	stomach
19	chr15:57598200-57599200	Active TSS	NHDF-Ad	bronchial
20	chr15:57598200-57599400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr15:57598200-57599400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:57598200-57599400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr15:57598200-57599400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:57598200-57599400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:57598200-57599400	Flanking Active TSS	Liver	Liver
26	chr15:57598200-57599400	Active TSS	Colon Smooth Muscle	Colon
27	chr15:57598200-57599400	Active TSS	Fetal Brain Female	brain
28	chr15:57598200-57599400	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr15:57598200-57599400	Flanking Active TSS	Fetal Stomach	stomach
30	chr15:57598200-57599400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr15:57598200-57599400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr15:57598200-57599600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr15:57598200-57599600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr15:57598200-57599600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:57598200-57599600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:57598200-57599600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:57598200-57599600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr15:57598200-57599600	Flanking Active TSS	Colonic Mucosa	Colon
39	chr15:57598200-57599600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr15:57598200-57599600	Enhancers	Spleen	Spleen
41	chr15:57598200-57599600	Flanking Active TSS	GM12878-XiMat	blood
42	chr15:57598200-57599800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr15:57598200-57600000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:57598400-57599000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:57598400-57599000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr15:57598400-57599000	Active TSS	Fetal Kidney	kidney
47	chr15:57598400-57599000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr15:57598400-57599000	Flanking Active TSS	Dnd41	blood
49	chr15:57598400-57599000	Flanking Active TSS	HepG2	liver
50	chr15:57598400-57599200	Active TSS	H1 Cell Line	embryonic stem cell

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