Variant report

Variant	rs7163020
Chromosome Location	chr15:39888068-39888069
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:39887671-39889275	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:39887532-39889262	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:39887572-39888998	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
5	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
6	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:39887981-39888118	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:39887692-39889213	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:39887473-39888568	HUVEC	blood vessel:	n/a	n/a
10	USF2	chr15:39887856-39888282	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr15:39888057-39889104	PBDE	blood:	n/a	n/a
12	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr15:39887322-39891967	MCF-7	breast:	n/a	n/a
15	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
17	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
19	POLR2A	chr15:39887688-39888309	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:39887720-39888564	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr15:39887700-39889084	A549	lung:	n/a	n/a
22	GATA3	chr15:39888058-39889104	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr15:39887685-39889294	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:39888049-39888099	HPAEpiC	pulmonary alveolar:	n/a
2	chr15:39888049-39888099	HMEC	breast:	n/a
3	chr15:39888049-39888099	SK-N-SH_RA	brain:	n/a
4	chr15:39888049-39888099	HL-60	blood:	n/a
5	chr15:39888049-39888099	U87	brain:	n/a
6	chr15:39888049-39888099	BE2_C	brain:	n/a
7	chr15:39888049-39888099	NHBE	bronchial:	n/a
8	chr15:39888049-39888099	CMK	blood:	n/a
9	chr15:39888049-39888099	Caco-2	colon:	n/a
10	chr15:39888049-39888099	HRPEpiC	eye:	n/a
11	chr15:39888049-39888099	HEEpiC	esophagus:	n/a
12	chr15:39888049-39888099	K562	blood:	n/a
13	chr15:39888049-39888099	A549	lung:	n/a
14	chr15:39888049-39888099	HIPEpiC	eye:	n/a
15	chr15:39888049-39888099	PrEC	prostate:	n/a
16	chr15:39888049-39888099	MCF10A-Er-Src	breast:	n/a
17	chr15:39888049-39888099	GM12891	blood:	n/a
18	chr15:39888049-39888099	Hela-S3	cervix:	n/a
19	chr15:39888049-39888099	GM12892	blood:	n/a
20	chr15:39888049-39888099	NH-A	brain:	n/a
21	chr15:39888049-39888099	IMR90	lung:	fetal
22	chr15:39888049-39888099	AG10803	skin:	n/a
23	chr15:39888049-39888099	HUVEC	blood vessel:	n/a
24	chr15:39888049-39888099	HCT-116	colon:	n/a
25	chr15:39888049-39888099	HRCEpiC	kidney:	n/a
26	chr15:39888049-39888099	NB4	blood:	n/a
27	chr15:39888049-39888099	SK-N-MC	brain:	n/a
28	chr15:39888049-39888099	MCF-7	breast:	n/a
29	chr15:39888049-39888099	ProgFib	skin:	n/a
30	chr15:39888049-39888099	AG04450	lung:	fetal
31	chr15:39888049-39888099	PFSK-1	brain:	n/a
32	chr15:39888049-39888099	GM12878	blood:	n/a
33	chr15:39888049-39888099	AG09319	gingival:	n/a
34	chr15:39888049-39888099	Jurkat	blood:	n/a
35	chr15:39888049-39888099	GM06990	blood:	n/a
36	chr15:39888049-39888099	Hepatocyte	liver:	n/a
37	chr15:39888049-39888099	ECC-1	luminal epithelium:	n/a
38	chr15:39888049-39888099	GM19239	blood:	n/a
39	chr15:39888049-39888099	HCM	heart:	n/a
40	chr15:39888049-39888099	T-47D	breast:	n/a
41	chr15:39888049-39888099	PANC-1	pancreas:	n/a
42	chr15:39888049-39888099	HNPCEpiC	eye:	n/a
43	chr15:39888049-39888099	HAEpiC	amniotic membrane:	n/a
44	chr15:39888049-39888099	NT2-D1	testis:	n/a
45	chr15:39888049-39888099	HRE	kidney:	n/a
46	chr15:39888049-39888099	SKMC	muscle:	n/a
47	chr15:39888049-39888099	HCF	heart:	n/a
48	chr15:39888049-39888099	LNCaP	prostate:	n/a
49	chr15:39888049-39888099	SAEC	small airway:	n/a
50	chr15:39888049-39888099	NHDF-neo	bronchial:	n/a

(count:2 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10083552	1.00[EUR][1000 genomes]
rs16969307	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969335	1.00[TSI][hapmap]
rs16969352	1.00[TSI][hapmap]
rs16969364	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969365	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969384	0.85[YRI][hapmap];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	0.87[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	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59146042	1.00[EUR][1000 genomes]
rs61040173	1.00[EUR][1000 genomes]
rs7172057	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8029417	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030643	0.82[ASW][hapmap];1.00[TSI][hapmap];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:93 , 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	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:39876000-39888600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:39876200-39888200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:39877800-39888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:39877800-39888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:39878000-39888400	Strong transcription	Left Ventricle	heart
17	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:39878200-39888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:39878400-39888400	Strong transcription	NHEK	skin
20	chr15:39878600-39888400	Strong transcription	HepG2	liver
21	chr15:39878600-39888800	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr15:39879000-39888800	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:39879200-39888400	Strong transcription	Adipose Nuclei	Adipose
24	chr15:39879200-39888400	Strong transcription	Fetal Lung	lung
25	chr15:39879800-39889400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:39880200-39889400	ZNF genes & repeats	Fetal Intestine Large	intestine
27	chr15:39880800-39888600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:39880800-39890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:39881000-39888800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:39881400-39888400	Strong transcription	Right Ventricle	heart
31	chr15:39881400-39888800	Strong transcription	Liver	Liver
32	chr15:39881400-39889200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:39882000-39889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:39882200-39888200	Strong transcription	Esophagus	oesophagus
35	chr15:39882200-39888400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:39882200-39889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:39883000-39889000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:39883400-39888400	Strong transcription	Fetal Brain Female	brain
39	chr15:39883600-39888200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr15:39883600-39888400	Strong transcription	Rectal Smooth Muscle	rectum
41	chr15:39883800-39888200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:39884200-39888200	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:39884400-39889400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:39884800-39890600	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr15:39885200-39891000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:39885400-39888800	Strong transcription	HSMMtube	muscle
47	chr15:39885800-39888400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:39885800-39888400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:39886000-39888600	Genic enhancers	A549	lung
50	chr15:39886000-39889400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links