Variant report

Variant	rs16882488
Chromosome Location	chr5:9354640-9354641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:9348625..9351178-chr5:9354314..9356306,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10071408	1.00[JPT][hapmap]
rs10491236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs11745486	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs16882559	1.00[ASW][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2526124	0.87[CEU][hapmap]
rs3734151	1.00[JPT][hapmap]
rs3797996	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822788	1.00[JPT][hapmap]
rs4429819	1.00[JPT][hapmap]
rs4540155	1.00[JPT][hapmap]
rs4702624	0.85[CEU][hapmap]
rs6555601	1.00[JPT][hapmap]
rs6864327	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs6868377	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs765046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs805143	1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16882488	SCGB2A2	trans	brain	seeQTL
rs16882488	SCGB1D2	trans	brain	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9332800-9372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:9340600-9356600	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:9347000-9356200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:9347000-9356200	Weak transcription	Fetal Stomach	stomach
5	chr5:9347000-9356400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:9347000-9365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:9347400-9356400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:9349200-9357800	Weak transcription	Right Ventricle	heart
9	chr5:9349400-9354800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:9349400-9356400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:9349600-9356400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:9350000-9356600	Weak transcription	Brain Angular Gyrus	brain
13	chr5:9350800-9355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:9351000-9356400	Weak transcription	NH-A	brain
15	chr5:9351000-9358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:9351000-9358200	Weak transcription	NHLF	lung
17	chr5:9351000-9359000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:9351200-9356400	Weak transcription	Fetal Heart	heart
19	chr5:9352000-9356200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:9352200-9358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:9352200-9358800	Weak transcription	NHDF-Ad	bronchial
22	chr5:9352400-9356600	Weak transcription	Osteobl	bone
23	chr5:9352600-9355400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:9353400-9357200	Enhancers	Fetal Intestine Large	intestine
25	chr5:9353400-9357800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:9353600-9355800	Enhancers	Fetal Intestine Small	intestine
27	chr5:9354000-9355000	Enhancers	Fetal Lung	lung
28	chr5:9354200-9354800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:9354200-9354800	Enhancers	Esophagus	oesophagus
30	chr5:9354200-9355000	Enhancers	Liver	Liver
31	chr5:9354200-9357200	Enhancers	Placenta Amnion	Placenta Amnion
32	chr5:9354200-9358600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:9354400-9355400	Enhancers	Placenta	Placenta
34	chr5:9354400-9355600	Enhancers	HMEC	breast
35	chr5:9354400-9356000	Weak transcription	Fetal Kidney	kidney
36	chr5:9354600-9354800	Enhancers	Brain Hippocampus Middle	brain
37	chr5:9354600-9354800	Enhancers	Small Intestine	intestine
38	chr5:9354600-9355200	Enhancers	Pancreas	Pancrea
39	chr5:9354600-9355400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:9354600-9355400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:9354600-9355400	Enhancers	NHEK	skin
42	chr5:9354600-9355600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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