Variant report

Variant	rs684016
Chromosome Location	chr1:10537090-10537091
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:10536970-10537146	HepG2	liver:	n/a	n/a
2	CEBPB	chr1:10536999-10537126	K562	blood:	n/a	n/a
3	FOXA2	chr1:10536904-10537107	HepG2	liver:	n/a	n/a
4	CEBPB	chr1:10536907-10537254	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10536268..10539627-chr1:10553457..10556201,3	K562	blood:
2	chr1:10528950..10534210-chr1:10534257..10537658,6	K562	blood:
3	chr1:10536910..10540005-chr1:10543843..10547119,3	K562	blood:
4	chr1:10508871..10511200-chr1:10534992..10537583,2	K562	blood:

No data

Variant related genes	Relation type
DFFA	TF binding region
ENSG00000142655	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000241563	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11121579	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11584327	0.84[TSI][hapmap]
rs1203122	0.85[EUR][1000 genomes]
rs12565133	0.92[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1307485	0.92[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap]
rs17035189	0.83[TSI][hapmap]
rs2186949	0.81[EUR][1000 genomes]
rs2274985	0.84[TSI][hapmap]
rs2781233	0.96[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs481571	0.92[CEU][hapmap];0.80[GIH][hapmap]
rs491880	0.92[CEU][hapmap]
rs505141	0.92[CEU][hapmap];0.80[GIH][hapmap]
rs528713	0.92[CEU][hapmap];0.80[GIH][hapmap]
rs585406	0.84[EUR][1000 genomes]
rs586223	0.88[CEU][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap]
rs597441	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs602601	0.80[CEU][hapmap]
rs604369	0.84[TSI][hapmap]
rs604814	0.80[CEU][hapmap];0.91[TSI][hapmap]
rs607941	0.81[AFR][1000 genomes]
rs628462	0.85[CHB][hapmap]
rs634358	0.92[CEU][hapmap]
rs649101	0.88[CEU][hapmap];0.80[GIH][hapmap]
rs655271	0.92[EUR][1000 genomes]
rs663864	0.90[EUR][1000 genomes]
rs670666	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs672606	0.86[EUR][1000 genomes]
rs673254	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7543322	0.80[TSI][hapmap]
rs7548453	0.81[CEU][hapmap];0.85[TSI][hapmap]

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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs684016	PEX14	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10535800-10537200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:10535800-10555000	Weak transcription	Aorta	Aorta
3	chr1:10536000-10537200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr1:10536000-10537200	Flanking Active TSS	HepG2	liver
5	chr1:10536000-10537400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:10536000-10539200	Weak transcription	Lung	lung
7	chr1:10536000-10544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:10536000-10548200	Weak transcription	Ovary	ovary
9	chr1:10536000-10549800	Weak transcription	Gastric	stomach
10	chr1:10536000-10549800	Weak transcription	Left Ventricle	heart
11	chr1:10536000-10550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:10536000-10555000	Weak transcription	Esophagus	oesophagus
13	chr1:10536000-10555000	Weak transcription	HSMMtube	muscle
14	chr1:10536000-10555600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:10536200-10537800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:10536200-10538000	Enhancers	Adipose Nuclei	Adipose
17	chr1:10536200-10544400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:10536200-10544800	Weak transcription	Osteobl	bone
19	chr1:10536200-10555000	Weak transcription	NH-A	brain
20	chr1:10536400-10537200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:10536400-10537600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:10536400-10537600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:10536400-10537800	Enhancers	Fetal Intestine Large	intestine
24	chr1:10536400-10538200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:10536400-10539200	Weak transcription	Primary T cells from cord blood	blood
26	chr1:10536400-10541400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:10536400-10541600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:10536400-10544200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:10536400-10549400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:10536400-10549400	Weak transcription	A549	lung
31	chr1:10536400-10549600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:10536400-10549800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:10536400-10550000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:10536400-10550000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:10536400-10553000	Weak transcription	Psoas Muscle	Psoas
36	chr1:10536400-10554000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:10536400-10554600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:10536400-10554800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:10536400-10554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:10536400-10554800	Weak transcription	Fetal Brain Male	brain
41	chr1:10536400-10554800	Weak transcription	NHDF-Ad	bronchial
42	chr1:10536400-10555000	Weak transcription	Fetal Kidney	kidney
43	chr1:10536400-10555000	Weak transcription	HSMM	muscle
44	chr1:10536600-10537200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:10536600-10537400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:10536600-10537400	Weak transcription	HMEC	breast
47	chr1:10536600-10537600	Enhancers	K562	blood
48	chr1:10536600-10537600	Weak transcription	NHEK	skin
49	chr1:10536600-10537800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:10536600-10537800	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links