Variant report

Variant	rs6501873
Chromosome Location	chr17:66922993-66922994
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1596314	0.87[EUR][1000 genomes]
rs1838102	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4147976	0.84[TSI][hapmap]
rs4147977	0.82[TSI][hapmap]
rs4147980	0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6501853	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6501870	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6501871	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67022365	0.83[EUR][1000 genomes]
rs7212686	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767690	0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8077155	0.89[EUR][1000 genomes]

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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1061151	chr17:66881617-66973917	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv908699	chr17:66885526-66933003	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv908700	chr17:66885526-66985992	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv908701	chr17:66888346-66978319	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1066412	chr17:66897540-66954067	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv1846502	chr17:66899261-66966274	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1849165	chr17:66899261-66978319	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv908702	chr17:66899290-66933003	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv908703	chr17:66904001-66978319	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv575929	chr17:66906217-66923711	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6501873	CSH2	cis	cerebellum	SCAN
rs6501873	EFCAB3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66906600-66927400	Weak transcription	Aorta	Aorta
2	chr17:66906800-66928200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:66907000-66940800	Weak transcription	Spleen	Spleen
4	chr17:66907200-66923800	Strong transcription	Liver	Liver
5	chr17:66907800-66923000	Weak transcription	Fetal Stomach	stomach
6	chr17:66908000-66949000	Weak transcription	Right Ventricle	heart
7	chr17:66908200-66930000	Weak transcription	Brain Angular Gyrus	brain
8	chr17:66912400-66928400	Weak transcription	Colon Smooth Muscle	Colon
9	chr17:66914200-66923000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:66914400-66923000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:66914400-66930200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:66916200-66934200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:66916200-66949000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:66916200-66949400	Weak transcription	Fetal Muscle Leg	muscle
15	chr17:66916400-66923000	Weak transcription	Brain Substantia Nigra	brain
16	chr17:66916400-66928800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:66916400-66938600	Weak transcription	Psoas Muscle	Psoas
18	chr17:66916400-66949200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr17:66916400-66949400	Weak transcription	Osteobl	bone
20	chr17:66919400-66923600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:66920400-66923200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr17:66920600-66923000	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:66921000-66923000	Weak transcription	Brain Anterior Caudate	brain
24	chr17:66921000-66923400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:66921000-66927000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr17:66921200-66924400	Weak transcription	Ovary	ovary
27	chr17:66921200-66925000	Weak transcription	Left Ventricle	heart
28	chr17:66921200-66941000	Weak transcription	Fetal Heart	heart
29	chr17:66921800-66923400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr17:66921800-66923800	Enhancers	HUVEC	blood vessel
31	chr17:66921800-66924600	Enhancers	Adipose Nuclei	Adipose
32	chr17:66922800-66923000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:66922800-66923000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr17:66922800-66923400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr17:66922800-66924000	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links