Variant report

Variant	rs10043586
Chromosome Location	chr5:147243511-147243512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCGB3A2-2	chr5:147242868-147244700	NONHSAT104430

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10039761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10078349	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171507	0.86[LWK][hapmap]
rs13353996	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13355958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360178	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28401755	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28437385	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28479902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28570984	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28588162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28609427	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28613022	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28684497	1.00[EUR][1000 genomes]
rs28707309	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59404183	1.00[EUR][1000 genomes]
rs60735175	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147234200-147262400	Weak transcription	Right Atrium	heart
2	chr5:147238600-147248800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:147239800-147245600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
4	chr5:147239800-147248600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:147240000-147248800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:147240200-147243600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:147240400-147244200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:147240400-147244400	Weak transcription	Small Intestine	intestine
9	chr5:147240400-147244600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
10	chr5:147240400-147248600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:147240800-147244600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
12	chr5:147241400-147244200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:147241800-147243800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr5:147242600-147243600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:147242600-147243600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:147242600-147243800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr5:147242600-147244000	Enhancers	Fetal Stomach	stomach
18	chr5:147242600-147244200	Enhancers	Fetal Lung	lung
19	chr5:147242600-147245200	Genic enhancers	H1 Cell Line	embryonic stem cell
20	chr5:147242800-147244000	Enhancers	Colon Smooth Muscle	Colon
21	chr5:147242800-147244200	Genic enhancers	H9 Cell Line	embryonic stem cell
22	chr5:147243000-147243600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr5:147243000-147243800	Enhancers	Fetal Muscle Leg	muscle
24	chr5:147243000-147243800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr5:147243000-147244000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:147243000-147244600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr5:147243200-147243600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:147243200-147244000	Enhancers	Stomach Mucosa	stomach
29	chr5:147243400-147248800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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