Variant report

Variant	rs9304337
Chromosome Location	chr18:44493094-44493095
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	chr18:44491476..44494532-chr18:44496207..44498289,3	MCF-7	breast:
2	chr18:44492204..44495512-chr18:44495791..44498945,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078043	Chromatin interaction
ENSG00000167216	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10853544	0.93[EUR][1000 genomes]
rs10853545	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10853547	0.89[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs11082562	0.88[EUR][1000 genomes]
rs1539878	0.89[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1789152	0.93[EUR][1000 genomes]
rs1893427	0.93[EUR][1000 genomes]
rs1942248	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2010834	0.89[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2032215	0.92[CEU][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs2051292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2156050	0.92[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2187090	0.92[EUR][1000 genomes]
rs2187092	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2510443	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2510444	0.81[EUR][1000 genomes]
rs2571024	0.81[EUR][1000 genomes]
rs2571026	0.80[EUR][1000 genomes]
rs2576051	0.82[EUR][1000 genomes]
rs2956973	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2957007	0.80[EUR][1000 genomes]
rs3744863	0.81[EUR][1000 genomes]
rs3892820	0.94[EUR][1000 genomes]
rs4258717	0.93[EUR][1000 genomes]
rs4548968	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890341	0.88[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4890342	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4890699	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs4890703	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4890707	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs509647	0.85[EUR][1000 genomes]
rs512868	0.83[CHD][hapmap]
rs538221	0.81[EUR][1000 genomes]
rs553456	0.92[CEU][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs557089	0.81[EUR][1000 genomes]
rs557661	0.81[EUR][1000 genomes]
rs571181	0.82[EUR][1000 genomes]
rs577200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs605487	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs607780	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs626217	0.92[CEU][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs642897	0.92[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs643233	0.81[ASN][1000 genomes]
rs649076	0.89[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs6507709	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6507712	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6507714	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs658756	0.92[CEU][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs695001	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7227700	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7232114	0.85[CHD][hapmap];0.95[JPT][hapmap]
rs7234570	0.93[EUR][1000 genomes]
rs7240239	0.92[CEU][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs7244013	0.85[EUR][1000 genomes]
rs7244778	0.89[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7245049	0.85[EUR][1000 genomes]
rs8089938	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8091984	0.83[EUR][1000 genomes]
rs8095373	0.89[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs9304338	0.88[EUR][1000 genomes]
rs9304340	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs9945443	0.92[EUR][1000 genomes]
rs9962523	0.93[EUR][1000 genomes]
rs998819	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv2763189	chr18:44415779-44515384	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv833639	chr18:44426363-44552719	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1059378	chr18:44431832-44509052	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv522397	chr18:44451644-44516088	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv576813	chr18:44481641-44531283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9304337	ST8SIA5	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44469800-44493600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr18:44469800-44493800	Weak transcription	Lung	lung
3	chr18:44469800-44494600	Weak transcription	Fetal Brain Male	brain
4	chr18:44469800-44495200	Weak transcription	Hela-S3	cervix
5	chr18:44469800-44495400	Weak transcription	Brain Anterior Caudate	brain
6	chr18:44469800-44496000	Weak transcription	HSMMtube	muscle
7	chr18:44469800-44496400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr18:44470600-44495600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr18:44470800-44493200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr18:44470800-44495200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr18:44470800-44495600	Weak transcription	Thymus	Thymus
12	chr18:44470800-44495800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr18:44470800-44495800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:44470800-44495800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:44471000-44495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr18:44471000-44495400	Weak transcription	Fetal Thymus	thymus
17	chr18:44471000-44495600	Weak transcription	HUVEC	blood vessel
18	chr18:44471000-44495800	Weak transcription	HSMM	muscle
19	chr18:44471200-44493200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr18:44471200-44495400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:44471200-44495400	Weak transcription	Primary B cells from cord blood	blood
22	chr18:44472200-44493800	Weak transcription	Left Ventricle	heart
23	chr18:44473800-44493400	Weak transcription	Fetal Heart	heart
24	chr18:44474400-44493600	Weak transcription	HepG2	liver
25	chr18:44475600-44494200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr18:44482400-44495200	Weak transcription	Primary T cells from cord blood	blood
27	chr18:44483600-44495400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr18:44484000-44493400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:44484000-44495400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr18:44484000-44495800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr18:44486800-44493600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr18:44487000-44493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr18:44487200-44494600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr18:44487400-44496000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr18:44487600-44493200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:44487600-44495200	Weak transcription	Fetal Lung	lung
37	chr18:44487800-44493600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr18:44487800-44493600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr18:44487800-44493800	Weak transcription	Psoas Muscle	Psoas
40	chr18:44488000-44495200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr18:44488000-44495200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:44488000-44495200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:44488200-44494800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr18:44488400-44495200	Weak transcription	Colon Smooth Muscle	Colon
45	chr18:44488600-44495200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr18:44489600-44493400	Weak transcription	GM12878-XiMat	blood
47	chr18:44489600-44493600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr18:44489600-44493600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr18:44489600-44493600	Weak transcription	Brain Germinal Matrix	brain
50	chr18:44489600-44493800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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