Variant report

Variant	rs2999546
Chromosome Location	chr1:151907839-151907840
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151905962..151909275-chr1:152006477..152009403,3	K562	blood:
2	chr1:151903606..151908213-chr1:151959560..151963672,4	MCF-7	breast:
3	chr1:151906693..151908513-chr1:151954832..151956959,2	K562	blood:
4	chr1:151906991..151909574-chr1:152001582..152003967,2	K562	blood:
5	chr1:151875575..151878356-chr1:151906918..151909478,2	MCF-7	breast:
6	chr1:151906723..151908280-chr1:151976802..151979658,2	MCF-7	breast:
7	chr1:151906694..151908997-chr1:151910180..151912030,2	K562	blood:
8	chr1:151905903..151909731-chr1:151970506..151972835,3	MCF-7	breast:
9	chr1:151880963..151883717-chr1:151905153..151908931,5	MCF-7	breast:
10	chr1:151887596..151890530-chr1:151906696..151908653,2	MCF-7	breast:
11	chr1:151907075..151908631-chr1:151973771..151976149,2	MCF-7	breast:
12	chr1:151906698..151908862-chr1:151958837..151961038,2	K562	blood:
13	chr1:151905958..151908802-chr1:151940211..151943154,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038747	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1060870	0.85[AMR][1000 genomes]
rs10788817	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788818	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10788820	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204914	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204915	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589720	0.89[ASN][1000 genomes]
rs12067594	0.87[AMR][1000 genomes]
rs12116923	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12562586	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1387833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907040	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2130525	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279501	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2279502	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2337689	0.81[ASN][1000 genomes]
rs2338201	0.85[AMR][1000 genomes]
rs2338209	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932565	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932577	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932581	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2932583	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2932586	0.91[ASN][1000 genomes]
rs2999506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999508	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2999512	0.88[ASN][1000 genomes]
rs2999541	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999542	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999544	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999545	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007670	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007685	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007691	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3007711	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845409	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845713	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685187	0.83[AMR][1000 genomes]
rs6698740	0.85[AMR][1000 genomes]
rs7542137	0.87[AMR][1000 genomes]
rs9435963	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9435964	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9943281	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2999546	THEM4	cis	Nerve Tibial	GTEx
rs2999546	THEM4	cis	multi-tissue	Pritchard
rs2999546	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999546	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999546	THEM4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151906000-151908400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:151906000-151908600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:151906400-151909000	Enhancers	Fetal Intestine Small	intestine
4	chr1:151906600-151908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:151906600-151908200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:151906600-151908200	Enhancers	HSMM	muscle
7	chr1:151906800-151908000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:151906800-151908000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:151906800-151908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:151906800-151908000	Enhancers	NH-A	brain
11	chr1:151906800-151908000	Enhancers	NHEK	skin
12	chr1:151906800-151908200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:151906800-151908200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:151906800-151908200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:151906800-151908200	Enhancers	HUVEC	blood vessel
16	chr1:151906800-151908400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:151906800-151908400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:151906800-151908400	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:151906800-151908400	Enhancers	A549	lung
20	chr1:151906800-151908600	Enhancers	Fetal Intestine Large	intestine
21	chr1:151906800-151909800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:151907000-151909000	Weak transcription	Liver	Liver
23	chr1:151907000-151909200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:151907000-151913000	Weak transcription	NHDF-Ad	bronchial
25	chr1:151907000-151914000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:151907000-151917400	Weak transcription	Right Atrium	heart
27	chr1:151907200-151908000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:151907200-151909400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:151907400-151908000	Enhancers	Fetal Kidney	kidney
30	chr1:151907400-151908000	Enhancers	HSMMtube	muscle
31	chr1:151907400-151908200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:151907400-151909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:151907400-151909600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:151907600-151908200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:151907600-151916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:151907800-151908000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:151907800-151908000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:151907800-151908000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:151907800-151908000	Enhancers	Hela-S3	cervix
40	chr1:151907800-151908200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:151907800-151908200	Enhancers	Placenta	Placenta
42	chr1:151907800-151909200	Weak transcription	K562	blood
43	chr1:151907800-151913200	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links