Variant report

Variant	rs6816534
Chromosome Location	chr4:85621772-85621773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11725121	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12500519	0.83[EUR][1000 genomes]
rs12502294	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12502409	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12511112	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs13108722	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13118671	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs1484661	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16995920	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17009317	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs17009334	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2218323	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs2869216	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs3098928	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs35190829	0.82[EUR][1000 genomes]
rs36036245	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3747680	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6825852	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6829807	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6838727	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6847067	0.85[JPT][hapmap]
rs6847564	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6858666	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs72664928	0.83[EUR][1000 genomes]
rs7685537	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs7695054	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6816534	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85587800-85648400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:85596200-85634600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:85598600-85632800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:85602600-85630600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:85603400-85631600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:85603800-85643800	Weak transcription	Stomach Mucosa	stomach
7	chr4:85604400-85637600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
9	chr4:85604800-85631600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:85605000-85637000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:85607800-85636000	Strong transcription	Fetal Lung	lung
12	chr4:85609200-85627400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:85609800-85623400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:85611600-85636600	Strong transcription	Stomach Smooth Muscle	stomach
15	chr4:85611800-85630000	Strong transcription	Fetal Brain Female	brain
16	chr4:85612400-85628200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:85612600-85639600	Weak transcription	Fetal Heart	heart
18	chr4:85613400-85627800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:85613400-85643000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:85613400-85646200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:85613400-85646600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:85613400-85649400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:85613600-85650200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:85614400-85625000	Strong transcription	Fetal Stomach	stomach
25	chr4:85614400-85630200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:85615200-85625000	Strong transcription	Left Ventricle	heart
28	chr4:85616800-85646600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:85617000-85623400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:85617000-85623400	Weak transcription	HepG2	liver
31	chr4:85617000-85641800	Weak transcription	Psoas Muscle	Psoas
32	chr4:85617400-85621800	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:85617400-85621800	Weak transcription	Gastric	stomach
34	chr4:85617400-85622000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:85617400-85624400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:85617400-85624600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:85617400-85627600	Weak transcription	Right Ventricle	heart
38	chr4:85617400-85628400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:85617600-85624200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:85617600-85628400	Weak transcription	Colonic Mucosa	Colon
41	chr4:85618000-85622000	Weak transcription	Lung	lung
42	chr4:85618000-85626400	Weak transcription	HMEC	breast
43	chr4:85618200-85622000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:85618200-85624600	Weak transcription	NHEK	skin
45	chr4:85618400-85621800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:85618400-85622000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:85619200-85622400	Strong transcription	Aorta	Aorta
48	chr4:85619200-85623200	Weak transcription	HUVEC	blood vessel
49	chr4:85619200-85636800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix

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