Variant report

Variant	rs4241122
Chromosome Location	chr2:113678856-113678857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11676778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708925	0.87[CHD][hapmap]
rs2708933	0.85[EUR][1000 genomes]
rs2723154	0.84[ASN][1000 genomes]
rs2723176	0.87[CHD][hapmap]
rs2723186	0.87[CHD][hapmap]
rs2723196	0.87[CHD][hapmap]
rs3811045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811046	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811048	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4074747	0.86[CHB][hapmap]
rs4289204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717710	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7564181	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	nsv961338	chr2:113657963-113691422	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003372	chr2:113670890-113682621	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4241122	TTL	cis	occipital cortex	BrainEAC

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113671600-113683000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:113674200-113679400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:113674400-113683000	Weak transcription	Gastric	stomach
4	chr2:113677200-113679000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:113677200-113681800	Weak transcription	Stomach Mucosa	stomach
6	chr2:113678000-113679000	Enhancers	NHEK	skin
7	chr2:113678000-113679200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:113678200-113679000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:113678200-113679200	Enhancers	HMEC	breast
10	chr2:113678200-113683400	Enhancers	Fetal Intestine Small	intestine
11	chr2:113678400-113679000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:113678400-113679000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:113678400-113679000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:113678400-113679200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:113678600-113680800	Enhancers	Fetal Intestine Large	intestine
16	chr2:113678800-113680600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:113678800-113680600	Weak transcription	K562	blood
18	chr2:113678800-113683400	Enhancers	Rectal Mucosa Donor 31	rectum

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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