Variant report

Variant	rs40669
Chromosome Location	chr5:9222811-9222812
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10079121	0.80[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs40665	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs40666	0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs40667	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs40669	SRD5A1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
3	chr5:9175600-9227400	Weak transcription	Colonic Mucosa	Colon
4	chr5:9185400-9264600	Weak transcription	Left Ventricle	heart
5	chr5:9189400-9228200	Weak transcription	Right Ventricle	heart
6	chr5:9190600-9228600	Weak transcription	Esophagus	oesophagus
7	chr5:9192800-9239600	Weak transcription	Pancreas	Pancrea
8	chr5:9197400-9223800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:9202400-9223600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:9211000-9224600	Weak transcription	NHLF	lung
11	chr5:9211000-9233000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:9211800-9244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:9213600-9226600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:9214200-9227400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:9215400-9224600	Weak transcription	Osteobl	bone
16	chr5:9218600-9239200	Weak transcription	Fetal Lung	lung
17	chr5:9218800-9226400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:9219400-9228600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:9219400-9229600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:9220600-9226400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:9220800-9223000	Strong transcription	Fetal Intestine Small	intestine
22	chr5:9220800-9225200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:9220800-9226400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:9221000-9230800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:9221000-9238200	Weak transcription	Aorta	Aorta
26	chr5:9221800-9223000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:9221800-9223400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:9222000-9223000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:9222000-9223000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr5:9222000-9223000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:9222000-9223200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr5:9222000-9223200	Enhancers	H9 Cell Line	embryonic stem cell
33	chr5:9222000-9223200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:9222000-9223400	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr5:9222000-9225000	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr5:9222000-9234200	Weak transcription	Fetal Kidney	kidney
37	chr5:9222200-9223000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr5:9222200-9223000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr5:9222200-9223400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:9222200-9223600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:9222200-9224000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:9222200-9225200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:9222400-9223000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr5:9222400-9223000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:9222400-9223600	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:9222400-9224800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:9222600-9223000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:9222600-9223000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
49	chr5:9222600-9224600	Weak transcription	Liver	Liver
50	chr5:9222600-9225200	Strong transcription	Fetal Heart	heart

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