Variant report

Variant	rs2218323
Chromosome Location	chr4:85626818-85626819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:85625865..85627430-chr4:85627945..85630287,2	K562	blood:
2	chr4:85502666..85505023-chr4:85626354..85628709,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163624	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10007879	0.86[EUR][1000 genomes]
rs11097024	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12511112	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13118671	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs13145705	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1385263	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1484661	0.91[JPT][hapmap]
rs17009247	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009249	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009317	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs17009334	0.90[JPT][hapmap]
rs2046404	0.86[JPT][hapmap]
rs2170935	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2869216	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap]
rs3098928	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36036245	0.82[EUR][1000 genomes]
rs3747680	0.89[CHD][hapmap];0.91[JPT][hapmap]
rs4529041	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531775	0.87[EUR][1000 genomes]
rs6825852	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs6829807	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs6835046	0.80[EUR][1000 genomes]
rs6838727	0.80[CHD][hapmap];0.91[JPT][hapmap]
rs6839516	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847067	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6847564	0.95[JPT][hapmap]
rs6853486	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs6858666	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs72664926	0.81[EUR][1000 genomes]
rs7668460	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7685537	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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
rs2218323	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	chr4:85611600-85636600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr4:85611800-85630000	Strong transcription	Fetal Brain Female	brain
15	chr4:85612400-85628200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:85612600-85639600	Weak transcription	Fetal Heart	heart
17	chr4:85613400-85627800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:85613400-85643000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:85613400-85646200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:85613400-85646600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:85613400-85649400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr4:85613600-85650200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:85614400-85630200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:85616800-85646600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:85617000-85641800	Weak transcription	Psoas Muscle	Psoas
27	chr4:85617400-85627600	Weak transcription	Right Ventricle	heart
28	chr4:85617400-85628400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:85617600-85628400	Weak transcription	Colonic Mucosa	Colon
30	chr4:85619200-85636800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
32	chr4:85619400-85630200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:85619400-85631000	Strong transcription	Fetal Muscle Leg	muscle
34	chr4:85619400-85636600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:85619400-85639000	Strong transcription	Adipose Nuclei	Adipose
36	chr4:85619400-85646400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr4:85619600-85630200	Strong transcription	Brain Hippocampus Middle	brain
38	chr4:85619600-85630200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:85619600-85638400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:85619600-85646400	Strong transcription	Liver	Liver
41	chr4:85619800-85631000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr4:85620000-85630200	Strong transcription	Brain Anterior Caudate	brain
43	chr4:85620000-85636000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:85620200-85629400	Strong transcription	Osteobl	bone
45	chr4:85620200-85629800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:85620200-85630200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:85620200-85632600	Strong transcription	HSMMtube	muscle
48	chr4:85620200-85635800	Strong transcription	Brain Germinal Matrix	brain
49	chr4:85620200-85640000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:85620200-85648000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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