Variant report

Variant	rs16969365
Chromosome Location	chr15:39887120-39887121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
2	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
3	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
4	FOS	chr15:39887088-39887171	MCF10A-Er-Src	breast:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
5	JUND	chr15:39886481-39887466	SK-N-SH	brain:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
6	FOSL2	chr15:39886936-39887314	SK-N-SH	brain:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
7	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:39886955-39887166	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
12	FOS	chr15:39886982-39887180	MCF10A-Er-Src	breast:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
13	JUND	chr15:39886746-39887421	SK-N-SH	brain:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
14	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
16	E2F4	chr15:39887081-39887314	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr15:39886757-39887442	SK-N-SH	brain:	n/a	n/a
18	PBX3	chr15:39886827-39887342	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr15:39877424-39887319	HepG2	liver:	n/a	n/a
20	GATA3	chr15:39886889-39887400	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
22	NFIC	chr15:39886741-39887472	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr15:39886907-39887478	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:39884658-39887138	HepG2	liver:	n/a	n/a
25	FOS	chr15:39886970-39887287	MCF10A-Er-Src	breast:	n/a	chr15:39887121-39887131 chr15:39887121-39887131
26	POLR2A	chr15:39885247-39887173	A549	lung:	n/a	n/a
27	FOS	chr15:39886980-39887275	MCF10A-Er-Src	breast:	n/a	chr15:39887121-39887131 chr15:39887121-39887131

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39885481..39888433-chr15:39892783..39894545,2	K562	blood:
2	chr15:39886322..39888433-chr15:39891587..39894545,2	K562	blood:

Variant related genes	Relation type
ENSG00000259279	TF binding region
ENSG00000150667	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10083552	1.00[EUR][1000 genomes]
rs16969307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969364	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969384	0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16969484	1.00[EUR][1000 genomes]
rs16969573	1.00[EUR][1000 genomes]
rs35248254	1.00[AMR][1000 genomes]
rs41376748	1.00[EUR][1000 genomes]
rs41406047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41515347	1.00[EUR][1000 genomes]
rs58677957	1.00[EUR][1000 genomes]
rs58716252	1.00[EUR][1000 genomes]
rs59146042	1.00[EUR][1000 genomes]
rs61040173	1.00[EUR][1000 genomes]
rs7163020	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172057	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8029417	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030643	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8031289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8033803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037769	1.00[AMR][1000 genomes]
rs8043342	1.00[EUR][1000 genomes]
rs878941	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
2	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
3	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:39877000-39887600	Weak transcription	Brain Germinal Matrix	brain
15	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:39877800-39887200	Weak transcription	Fetal Thymus	thymus
17	chr15:39877800-39888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:39877800-39888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:39878000-39888400	Strong transcription	Left Ventricle	heart
20	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:39878200-39888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:39878400-39888400	Strong transcription	NHEK	skin
23	chr15:39878600-39888400	Strong transcription	HepG2	liver
24	chr15:39878600-39888800	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr15:39879000-39888800	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:39879200-39888400	Strong transcription	Adipose Nuclei	Adipose
27	chr15:39879200-39888400	Strong transcription	Fetal Lung	lung
28	chr15:39879800-39889400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:39880000-39888000	Strong transcription	Fetal Heart	heart
30	chr15:39880200-39889400	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr15:39880600-39887800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:39880600-39887800	Strong transcription	Ovary	ovary
33	chr15:39880800-39888600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr15:39880800-39890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:39881000-39888800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:39881400-39888400	Strong transcription	Right Ventricle	heart
37	chr15:39881400-39888800	Strong transcription	Liver	Liver
38	chr15:39881400-39889200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:39882000-39889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:39882200-39887600	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:39882200-39888200	Strong transcription	Esophagus	oesophagus
42	chr15:39882200-39888400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr15:39882200-39889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:39883000-39889000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:39883400-39888400	Strong transcription	Fetal Brain Female	brain
46	chr15:39883600-39888200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:39883600-39888400	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:39883800-39888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:39884000-39888000	Weak transcription	Thymus	Thymus
50	chr15:39884200-39888200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links