Variant report

Variant	rs2999554
Chromosome Location	chr1:152013532-152013533
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151958520..151979218-chr1:151992734..152014750,97	MCF-7	breast:
2	chr1:152012471..152014321-chr1:152084616..152087281,2	MCF-7	breast:
3	chr1:152013400..152016839-chr1:152017055..152020661,5	K562	blood:
4	chr1:152012090..152014463-chr17:57922085..57923933,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229021	Chromatin interaction
ENSG00000159450	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1496037	0.95[ASN][1000 genomes]
rs2999547	0.87[ASN][1000 genomes]
rs2999551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999552	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2999553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999555	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2999562	1.00[ASN][1000 genomes]
rs3007672	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007673	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007676	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3007677	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3007678	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007679	0.84[EUR][1000 genomes]
rs3104205	0.81[ASN][1000 genomes]
rs3122300	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3122301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3122302	0.87[EUR][1000 genomes]
rs3122303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122304	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811422	0.92[AMR][1000 genomes];0.97[EUR][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	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
5	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2999554	LOC729659///LOC730278	trans	lymphoblastoid	RTeQTL
rs2999554	S100A11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152009600-152019800	Weak transcription	Small Intestine	intestine
2	chr1:152010000-152013800	Enhancers	Fetal Thymus	thymus
3	chr1:152010000-152016400	Weak transcription	Adipose Nuclei	Adipose
4	chr1:152010000-152017000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:152010000-152018400	Weak transcription	A549	lung
6	chr1:152010000-152018400	Weak transcription	NHEK	skin
7	chr1:152010000-152019800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:152010000-152020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:152010200-152014400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:152010200-152016000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:152010200-152020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:152010200-152020000	Weak transcription	Colonic Mucosa	Colon
13	chr1:152010200-152020400	Weak transcription	Gastric	stomach
14	chr1:152010800-152018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:152011200-152013600	Enhancers	Primary B cells from cord blood	blood
16	chr1:152011200-152016400	Weak transcription	Hela-S3	cervix
17	chr1:152011400-152019600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:152012000-152015200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:152012600-152019200	Weak transcription	Esophagus	oesophagus
20	chr1:152012800-152016200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:152012800-152019600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:152012800-152019600	Weak transcription	Thymus	Thymus
23	chr1:152013000-152014400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr1:152013000-152016000	Weak transcription	Fetal Intestine Large	intestine
25	chr1:152013200-152018600	Weak transcription	K562	blood
26	chr1:152013400-152013800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links