Variant report

Variant	rs930484
Chromosome Location	chr15:99961684-99961685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99960171..99963200-chr15:100104719..100108193,3	MCF-7	breast:
2	chr15:99960211..99963086-chr15:99964919..99968237,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTC23-5	chr15:99961346-99963761	l_1247_chr15:99961345-99972053_liver

Variant related genes	Relation type
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12594256	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12898756	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4563026	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4965487	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56280996	0.90[ASN][1000 genomes]
rs6598242	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6598243	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6598244	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6598245	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7180263	0.83[EUR][1000 genomes]
rs8026539	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8026724	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs930482	0.89[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
10	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv904547	chr15:99940221-99979159	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv904548	chr15:99940221-99979418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv904549	chr15:99940221-99991506	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv519800	chr15:99950772-99987109	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv904550	chr15:99954278-99978524	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv904551	chr15:99954278-99979418	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv904552	chr15:99954278-99982447	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv904553	chr15:99954278-99983175	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv904554	chr15:99956954-99979418	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv904555	chr15:99956954-99981269	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv904556	chr15:99956954-99987109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv904557	chr15:99956954-99991506	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99944800-99972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:99950000-99964800	Weak transcription	Adipose Nuclei	Adipose
3	chr15:99950800-99965800	Weak transcription	Aorta	Aorta
4	chr15:99951000-99965200	Weak transcription	Spleen	Spleen
5	chr15:99953000-99965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:99955400-99964200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:99955600-99963400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:99955600-99963600	Weak transcription	Left Ventricle	heart
9	chr15:99956400-99963400	Weak transcription	Esophagus	oesophagus
10	chr15:99957000-99964200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:99957000-99964200	Weak transcription	Lung	lung
12	chr15:99957200-99965200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:99957200-99973200	Weak transcription	Gastric	stomach
14	chr15:99960800-99965000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:99961000-99962400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr15:99961000-99965000	Enhancers	Primary T cells from cord blood	blood
17	chr15:99961000-99966800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:99961200-99961800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:99961200-99961800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:99961400-99961800	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:99961400-99961800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr15:99961400-99961800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:99961400-99961800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:99961400-99961800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:99961400-99961800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr15:99961400-99961800	Enhancers	Placenta	Placenta
27	chr15:99961400-99961800	Enhancers	Fetal Stomach	stomach
28	chr15:99961400-99961800	Enhancers	Pancreas	Pancrea
29	chr15:99961400-99961800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr15:99961400-99962000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:99961400-99962000	Enhancers	Fetal Thymus	thymus
32	chr15:99961400-99962800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:99961400-99965200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr15:99961600-99961800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:99961600-99961800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:99961600-99961800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:99961600-99961800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr15:99961600-99961800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr15:99961600-99961800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:99961600-99961800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:99961600-99961800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:99961600-99961800	Enhancers	Colonic Mucosa	Colon
43	chr15:99961600-99961800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr15:99961600-99961800	Enhancers	Stomach Mucosa	stomach
45	chr15:99961600-99962000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr15:99961600-99962000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr15:99961600-99962000	Enhancers	Fetal Intestine Small	intestine
48	chr15:99961600-99962000	Flanking Active TSS	HepG2	liver
49	chr15:99961600-99962400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr15:99961600-99962800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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