Variant report

Variant	rs982975
Chromosome Location	chr14:24863513-24863514
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr14:24863507-24863726	SK-N-SH_RA	brain:	n/a	n/a
2	RAD21	chr14:24863511-24863787	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr14:24863509-24863739	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr14:24863372-24863925	HCT-116	colon:	n/a	n/a
5	CTCF	chr14:24863364-24863904	MCF-7	breast:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24833467..24839902-chr14:24859160..24864405,20	MCF-7	breast:
2	chr14:24858434..24861313-chr14:24861700..24864239,2	K562	blood:
3	chr14:24857849..24868599-chr14:24892485..24903992,27	MCF-7	breast:
4	chr14:24861298..24864304-chr14:24910637..24912997,3	MCF-7	breast:
5	chr14:24842752..24851075-chr14:24856697..24867572,25	MCF-7	breast:
6	chr14:24863230..24864059-chr14:24881607..24882294,2	MCF-7	breast:
7	chr14:24862205..24864720-chr14:24888847..24891596,2	K562	blood:
8	chr14:24842116..24850865-chr14:24857760..24868159,21	MCF-7	breast:
9	chr14:24860841..24863553-chr14:24881308..24883700,2	MCF-7	breast:
10	chr14:24834637..24835255-chr14:24863250..24863914,2	MCF-7	breast:
11	chr14:24801726..24804561-chr14:24861789..24863588,2	MCF-7	breast:
12	chr14:24860308..24863540-chr14:24898035..24902526,6	MCF-7	breast:
13	chr14:24861396..24863680-chr14:24873747..24875819,2	MCF-7	breast:
14	chr14:24860191..24864125-chr14:24897028..24901023,4	K562	blood:

No data

Variant related genes	Relation type
NYNRIN	TF binding region
ENSG00000100441	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000100968	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10129213	0.82[CHB][hapmap]
rs11846223	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11851567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2243891	0.82[CHB][hapmap]
rs2332327	0.82[CHB][hapmap]
rs57437663	0.85[ASN][1000 genomes]
rs58583694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954134	0.82[CHB][hapmap]

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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs982975	OR4K17	cis	cerebellum	SCAN
rs982975	OR4L1	cis	parietal	SCAN
rs982975	PABPN1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24859000-24865000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr14:24859000-24867000	Weak transcription	Right Atrium	heart
3	chr14:24859200-24866200	Weak transcription	Fetal Stomach	stomach
4	chr14:24859200-24867200	Weak transcription	NHLF	lung
5	chr14:24860400-24864800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:24860800-24864400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr14:24860800-24864600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr14:24860800-24864800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:24860800-24864800	Weak transcription	Gastric	stomach
10	chr14:24860800-24867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:24860800-24867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr14:24860800-24867600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr14:24860800-24868000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr14:24861000-24865400	Weak transcription	Lung	lung
15	chr14:24861400-24863800	Enhancers	Fetal Lung	lung
16	chr14:24861800-24864600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr14:24861800-24866800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr14:24862000-24864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:24862000-24867600	Weak transcription	Small Intestine	intestine
20	chr14:24862000-24867600	Weak transcription	A549	lung
21	chr14:24862200-24864800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:24862200-24864800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr14:24862200-24864800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:24862200-24865000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:24862200-24865000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr14:24862200-24865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:24862200-24865200	Weak transcription	Stomach Mucosa	stomach
28	chr14:24862200-24865400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr14:24862200-24865400	Weak transcription	NHDF-Ad	bronchial
30	chr14:24862200-24865800	Weak transcription	K562	blood
31	chr14:24862200-24866600	Weak transcription	Fetal Kidney	kidney
32	chr14:24862200-24866800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:24862200-24867000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:24862200-24867000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr14:24862200-24867200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:24862400-24864600	Weak transcription	NHEK	skin
37	chr14:24862400-24864800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr14:24862400-24864800	Weak transcription	Placenta	Placenta
39	chr14:24862400-24864800	Weak transcription	HMEC	breast
40	chr14:24862400-24865400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:24862400-24866800	Weak transcription	Fetal Intestine Large	intestine
42	chr14:24862400-24867000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr14:24862400-24867000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr14:24862400-24867200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr14:24862400-24867200	Weak transcription	HUVEC	blood vessel
46	chr14:24862400-24867800	Weak transcription	Osteobl	bone
47	chr14:24862600-24867000	Weak transcription	Fetal Brain Female	brain
48	chr14:24863200-24863800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:24863200-24865800	Enhancers	Primary hematopoietic stem cells	blood
50	chr14:24863200-24866600	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links