Variant report

Variant	rs2055498
Chromosome Location	chr1:47489001-47489002
allele	A/G
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	TCF7L2	chr1:47488638-47489349	HEK293	kidney:	n/a	n/a
2	SETDB1	chr1:47488552-47489130	U2OS	brain:	n/a	n/a
3	STAT3	chr1:47488982-47489107	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF263	chr1:47488839-47490425	HEK293-T-REx	kidney:	n/a	chr1:47489677-47489698
5	CTCF	chr1:47488920-47489070	HEK293	kidney:	n/a	n/a
6	E2F6	chr1:47488602-47489632	H1-hESC	embryonic stem cell:	n/a	chr1:47489442-47489454 chr1:47489421-47489433
7	KAP1	chr1:47488791-47489506	U2OS	brain:	n/a	n/a
8	REST	chr1:47488528-47490139	H1-neurons	neurons:	n/a	chr1:47489332-47489345

Variant related genes	Relation type
CYP4X1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11211420	1.00[MEX][hapmap]
rs11582907	0.91[MEX][hapmap]
rs12403250	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404930	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12408938	0.81[YRI][hapmap]
rs17102950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202222	1.00[MEX][hapmap]
rs2292059	1.00[MEX][hapmap]
rs2292060	1.00[MEX][hapmap]
rs56079820	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74073804	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9699826	0.91[MEX][hapmap]
rs9727254	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9793231	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9793989	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv546166	chr1:47407739-47495605	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47487800-47489200	Weak transcription	Lung	lung
2	chr1:47487800-47489200	Weak transcription	Right Atrium	heart
3	chr1:47488600-47489200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
4	chr1:47488600-47489600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr1:47488800-47489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:47488800-47489200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr1:47488800-47489200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr1:47488800-47489200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr1:47488800-47489200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:47488800-47489200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
11	chr1:47488800-47489200	Bivalent Enhancer	Left Ventricle	heart
12	chr1:47488800-47489200	Enhancers	Pancreas	Pancrea
13	chr1:47488800-47489200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:47488800-47489400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
15	chr1:47488800-47489600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
16	chr1:47488800-47489800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
17	chr1:47488800-47490000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:47488800-47490000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:47488800-47490000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:47488800-47490000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:47488800-47490400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:47488800-47490400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:47488800-47490600	Active TSS	Brain Anterior Caudate	brain
24	chr1:47489000-47489200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:47489000-47489200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:47489000-47489200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:47489000-47489200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:47489000-47489200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:47489000-47489200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
30	chr1:47489000-47489200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
31	chr1:47489000-47489200	Bivalent Enhancer	HMEC	breast
32	chr1:47489000-47489200	Flanking Active TSS	NHEK	skin
33	chr1:47489000-47489400	Enhancers	Liver	Liver
34	chr1:47489000-47489400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:47489000-47489400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
36	chr1:47489000-47489400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
37	chr1:47489000-47489600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:47489000-47489800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:47489000-47489800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:47489000-47489800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:47489000-47489800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:47489000-47490000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr1:47489000-47490000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:47489000-47490000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr1:47489000-47490000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr1:47489000-47490000	Active TSS	Psoas Muscle	Psoas
47	chr1:47489000-47490200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:47489000-47490200	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr1:47489000-47490200	Bivalent/Poised TSS	Fetal Kidney	kidney
50	chr1:47489000-47490200	Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links