Variant report

Variant	rs42564
Chromosome Location	chr5:16722140-16722141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs152726	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs153182	0.89[ASN][1000 genomes]
rs153183	0.84[ASN][1000 genomes]
rs153184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs153185	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs173738	0.89[LWK][hapmap]
rs17501392	0.86[JPT][hapmap]
rs193924	0.96[ASN][1000 genomes]
rs250343	0.85[ASW][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs26740	0.84[LWK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs27552	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs31290	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs31293	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs31296	0.84[AFR][1000 genomes]
rs31297	0.84[AFR][1000 genomes]
rs31299	0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs31497	0.87[ASN][1000 genomes]
rs39887	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs39889	0.88[ASN][1000 genomes]
rs40979	1.00[ASW][hapmap];0.94[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:16710400-16723600	Weak transcription	Esophagus	oesophagus
3	chr5:16711200-16723800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
5	chr5:16711400-16724000	Weak transcription	Ovary	ovary
6	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
8	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:16711400-16731800	Weak transcription	HMEC	breast
10	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
11	chr5:16713800-16731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:16713800-16735600	Weak transcription	Colonic Mucosa	Colon
13	chr5:16714000-16724000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:16714000-16726200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:16714000-16726200	Weak transcription	Left Ventricle	heart
16	chr5:16714000-16730200	Weak transcription	Osteobl	bone
17	chr5:16714200-16726200	Weak transcription	Fetal Kidney	kidney
18	chr5:16714200-16730400	Weak transcription	NHLF	lung
19	chr5:16714200-16736000	Weak transcription	NHDF-Ad	bronchial
20	chr5:16714400-16730000	Weak transcription	NH-A	brain
21	chr5:16714600-16726400	Weak transcription	Brain Substantia Nigra	brain
22	chr5:16714600-16728200	Weak transcription	Psoas Muscle	Psoas
23	chr5:16715000-16725400	Weak transcription	HUVEC	blood vessel
24	chr5:16719400-16722400	Enhancers	Pancreas	Pancrea
25	chr5:16719400-16723000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr5:16719600-16722600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:16719800-16722600	Enhancers	Fetal Intestine Large	intestine
28	chr5:16719800-16722800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:16720000-16722600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:16720000-16722800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:16720000-16723200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:16720200-16722600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr5:16720200-16722600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:16720200-16722600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:16720200-16722600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:16720400-16722400	Enhancers	Fetal Intestine Small	intestine
37	chr5:16720600-16722800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:16720800-16722800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr5:16720800-16723000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:16721000-16722200	Flanking Active TSS	HepG2	liver
41	chr5:16721000-16722400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr5:16721000-16722600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr5:16721000-16723000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:16721000-16724800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:16721200-16722200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:16721200-16722400	Enhancers	Brain Hippocampus Middle	brain
47	chr5:16721200-16723000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr5:16721400-16722400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr5:16721400-16723200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr5:16721400-16725800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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