Variant report

Variant	rs1904454
Chromosome Location	chr5:9149422-9149423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12189232	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs12519438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179890	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs168817	0.92[CEU][hapmap]
rs1806151	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2256569	0.81[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap]
rs2456237	0.92[CEU][hapmap]
rs253633	0.96[CEU][hapmap]
rs253634	0.85[CEU][hapmap]
rs253635	0.96[CEU][hapmap]
rs253638	0.85[CEU][hapmap]
rs253644	0.82[CEU][hapmap]
rs253645	0.96[CEU][hapmap]
rs253646	0.96[CEU][hapmap]
rs253647	0.81[EUR][1000 genomes]
rs253648	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253649	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253652	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs253653	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6862429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6863413	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs975096	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv880683	chr5:9091164-9170323	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv881682	chr5:9100211-9151237	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv880323	chr5:9100211-9157454	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1904454	SRD5A1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9119200-9153200	Weak transcription	Fetal Intestine Large	intestine
2	chr5:9119400-9151800	Weak transcription	Left Ventricle	heart
3	chr5:9119400-9152000	Weak transcription	Right Ventricle	heart
4	chr5:9119400-9152000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:9134000-9152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:9134400-9156600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
9	chr5:9137000-9151800	Weak transcription	Fetal Heart	heart
10	chr5:9141200-9154400	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:9143600-9161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:9145000-9154400	Weak transcription	Aorta	Aorta
13	chr5:9145000-9154400	Weak transcription	Liver	Liver
14	chr5:9145000-9154400	Weak transcription	Fetal Stomach	stomach
15	chr5:9145000-9158000	Weak transcription	Esophagus	oesophagus
16	chr5:9145200-9152200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:9145200-9157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:9145200-9160800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:9145400-9163200	Weak transcription	Fetal Kidney	kidney
20	chr5:9145600-9152000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:9145600-9152000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:9145800-9150600	Weak transcription	Fetal Intestine Small	intestine
24	chr5:9146400-9152000	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:9147200-9151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:9147200-9152000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:9147400-9150000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:9147400-9151800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:9147600-9152600	Enhancers	NHDF-Ad	bronchial
30	chr5:9147800-9151000	Enhancers	NHLF	lung
31	chr5:9148000-9150000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:9148000-9151000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:9148000-9151200	Enhancers	HMEC	breast
34	chr5:9148000-9151200	Enhancers	NHEK	skin
35	chr5:9148200-9151400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:9148400-9151200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:9148600-9155600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:9148800-9149800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:9148800-9149800	Weak transcription	NH-A	brain
40	chr5:9148800-9149800	Weak transcription	Osteobl	bone
41	chr5:9148800-9150000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:9148800-9150000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:9148800-9152000	Weak transcription	Spleen	Spleen
44	chr5:9148800-9153000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:9149200-9149600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:9149400-9149600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:9149400-9150800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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