Variant report

Variant	rs4779842
Chromosome Location	chr15:31514456-31514457
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	chr15:31505148..31511050-chr15:31511462..31517687,6	K562	blood:
2	chr15:31513902..31515843-chr15:31521318..31523081,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRPM1-1	chr15:31514042-31515539	XLOC_011413
2	lnc-TRPM1-1	chr15:31514202-31514501	ENSG00000259772.1

Variant related genes	Relation type
ENSG00000259772	Chromatin interaction
ENSG00000259448	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11070871	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134444	0.88[ASN][1000 genomes]
rs4270138	0.99[ASN][1000 genomes]
rs4779841	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023548	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv903839	chr15:31495113-31576677	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv977067	chr15:31509197-31523063	Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31508400-31514600	Weak transcription	Small Intestine	intestine
2	chr15:31508400-31516000	Weak transcription	Aorta	Aorta
3	chr15:31509200-31515200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:31509200-31515200	Weak transcription	Right Ventricle	heart
5	chr15:31509200-31515400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:31509200-31515400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:31509200-31515400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:31509400-31514600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:31509400-31514600	Weak transcription	Brain Substantia Nigra	brain
10	chr15:31509400-31514800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:31509400-31514800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:31509400-31515200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:31509400-31515200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:31509400-31515200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:31509400-31515200	Weak transcription	Colonic Mucosa	Colon
16	chr15:31509600-31514600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:31509600-31514600	Weak transcription	Liver	Liver
18	chr15:31509600-31515000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:31509600-31515400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:31509600-31520600	Weak transcription	HepG2	liver
21	chr15:31510400-31515000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:31510400-31515400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:31510800-31520600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:31511000-31515000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:31511000-31515200	Weak transcription	Left Ventricle	heart
26	chr15:31511000-31515400	Weak transcription	Right Atrium	heart
27	chr15:31511600-31515200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:31512200-31515600	Strong transcription	GM12878-XiMat	blood
29	chr15:31512800-31514600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:31513200-31518000	Enhancers	Fetal Thymus	thymus
31	chr15:31513800-31515600	Enhancers	Fetal Intestine Large	intestine
32	chr15:31513800-31517400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr15:31514000-31515600	Enhancers	Thymus	Thymus
34	chr15:31514000-31515800	Enhancers	Fetal Intestine Small	intestine
35	chr15:31514000-31516600	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:31514000-31516800	Enhancers	Primary hematopoietic stem cells	blood
37	chr15:31514000-31517600	Enhancers	Primary B cells from cord blood	blood
38	chr15:31514200-31514600	Genic enhancers	Gastric	stomach
39	chr15:31514200-31514600	Enhancers	Psoas Muscle	Psoas
40	chr15:31514200-31514600	Enhancers	A549	lung
41	chr15:31514200-31514800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr15:31514200-31515000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr15:31514200-31515200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr15:31514200-31515400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:31514200-31515600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr15:31514200-31515600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr15:31514200-31515600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:31514200-31515800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:31514200-31515800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr15:31514200-31516000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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