Variant report

Variant	rs17621117
Chromosome Location	chr7:40844275-40844276
allele	C/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	EP300	chr7:40844198-40844581	SK-N-SH_RA	brain:	n/a	n/a
2	PBX3	chr7:40844017-40845582	SK-N-SH	brain:	n/a	n/a
3	EP300	chr7:40844031-40844514	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chr7:40843871-40844821	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr7:40843891-40845419	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SUGCT	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1012567	1.00[YRI][hapmap]
rs10499618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12154576	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12155167	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13230202	1.00[YRI][hapmap]
rs17438725	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17439106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17439448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17439553	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17439595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17529882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17530234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17621020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17621508	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17688549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17688583	1.00[YRI][hapmap]
rs17688601	1.00[YRI][hapmap]
rs55641974	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55764442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55832912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55834632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55836921	0.82[ASN][1000 genomes]
rs55992488	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6970230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73689863	0.82[ASN][1000 genomes]
rs73689865	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73689870	0.82[ASN][1000 genomes]
rs73689875	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830972	chr7:40814709-40945917	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830973	chr7:40816419-40851594	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40835400-40847800	Weak transcription	Aorta	Aorta
2	chr7:40835800-40844400	Weak transcription	HSMM	muscle
3	chr7:40839800-40844600	Weak transcription	Fetal Stomach	stomach
4	chr7:40840000-40844400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:40840800-40844400	Weak transcription	Brain Substantia Nigra	brain
6	chr7:40841000-40844400	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:40841000-40844600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:40841000-40844600	Weak transcription	HSMMtube	muscle
9	chr7:40842400-40847200	Weak transcription	Ovary	ovary
10	chr7:40842400-40847600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:40842400-40847800	Weak transcription	HMEC	breast
12	chr7:40843400-40844600	Weak transcription	Colonic Mucosa	Colon
13	chr7:40843600-40844400	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr7:40843600-40844600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:40843600-40850000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:40844000-40844400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:40844000-40845600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:40844000-40846000	Enhancers	Osteobl	bone
19	chr7:40844200-40845400	Flanking Active TSS	NHDF-Ad	bronchial
20	chr7:40844200-40845600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:40844200-40845600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:40844200-40845600	Enhancers	NHLF	lung
23	chr7:40844200-40848600	Enhancers	Muscle Satellite Cultured Cells	--

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