Variant report

Variant	rs9889324
Chromosome Location	chr17:60126622-60126623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60120399..60123083-chr17:60125814..60127828,3	MCF-7	breast:
2	chr17:60123757..60127581-chr17:60130272..60133772,4	K562	blood:
3	chr17:60111538..60114046-chr17:60124883..60126946,2	MCF-7	breast:
4	chr17:60125809..60127843-chr17:60128789..60132797,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079461	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079464	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11649711	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11870331	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12450995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2048718	0.81[CHD][hapmap]
rs28610444	0.87[AMR][1000 genomes]
rs28755966	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4456566	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4479315	0.88[ASN][1000 genomes]
rs4493126	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968410	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4968466	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4968469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968477	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs58046762	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6504079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67274807	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs686994	0.83[JPT][hapmap]
rs7207930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7210061	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7218545	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7222262	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72845411	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72845416	0.82[EUR][1000 genomes]
rs72845417	0.82[EUR][1000 genomes]
rs72845418	0.82[EUR][1000 genomes]
rs8067092	0.80[CHD][hapmap]
rs8072101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8081805	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8081812	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap]
rs9303455	0.83[EUR][1000 genomes]
rs9747976	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9889676	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs9901321	0.82[EUR][1000 genomes]
rs9902812	0.94[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs9908352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9913443	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3415630	chr17:60124819-60401635	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9889324	MED13	cis	cerebellum	SCAN
rs9889324	MRPS23	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
2	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
3	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr17:60098800-60135000	Strong transcription	Dnd41	blood
5	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:60106000-60129800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:60109000-60128600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:60110600-60135200	Weak transcription	Aorta	Aorta
14	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
15	chr17:60111000-60130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:60111000-60133800	Weak transcription	Pancreas	Pancrea
17	chr17:60111200-60129000	Weak transcription	Brain Angular Gyrus	brain
18	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:60111400-60128200	Weak transcription	NHEK	skin
20	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain
21	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:60115000-60140000	Weak transcription	Gastric	stomach
24	chr17:60115200-60127800	Strong transcription	HepG2	liver
25	chr17:60115400-60128200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr17:60115400-60131400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr17:60115400-60135000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr17:60116000-60131000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:60116000-60139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:60116200-60139800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr17:60116400-60130600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr17:60116400-60133800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr17:60116600-60128400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:60116600-60131000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:60116600-60139000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:60116800-60129000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr17:60117000-60130800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr17:60117200-60130200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:60117200-60130600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr17:60117200-60133800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:60117200-60136800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr17:60117400-60139200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:60118000-60130800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:60118000-60135000	Strong transcription	Placenta	Placenta
45	chr17:60118200-60131200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:60118400-60129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr17:60119800-60136800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr17:60120000-60133600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:60120600-60136800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:60121000-60128600	Weak transcription	Small Intestine	intestine

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