Variant report

Variant	rs9908352
Chromosome Location	chr17:60118119-60118120
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60117240..60120020-chr17:60137315..60140366,3	MCF-7	breast:
2	chr17:60117810..60120671-chr17:60140883..60143140,2	K562	blood:
3	chr17:60109548..60112572-chr17:60115056..60118748,3	MCF-7	breast:
4	chr17:60116389..60118637-chr17:60141946..60144107,3	MCF-7	breast:
5	chr17:60117175..60120950-chr17:60121256..60123902,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11079464	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11870331	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[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];0.93[EUR][1000 genomes];0.89[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];0.93[EUR][1000 genomes];0.85[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];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4968477	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs6504077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[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];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210061	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7218545	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7222262	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067092	0.81[CHD][hapmap]
rs8072101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[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];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8081805	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][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]
rs9747976	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9889324	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]
rs9889676	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs9901321	0.86[EUR][1000 genomes]
rs9902812	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs9913443	1.00[ASW][hapmap];0.85[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9908352	MED13	cis	cerebellum	SCAN
rs9908352	MRPS23	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
3	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
4	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:60098800-60135000	Strong transcription	Dnd41	blood
6	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:60105600-60120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:60106000-60129800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr17:60109000-60119000	Weak transcription	Brain Germinal Matrix	brain
14	chr17:60109000-60119000	Weak transcription	Colonic Mucosa	Colon
15	chr17:60109000-60120200	Weak transcription	Small Intestine	intestine
16	chr17:60109000-60128600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:60110400-60123800	Weak transcription	Psoas Muscle	Psoas
19	chr17:60110600-60135200	Weak transcription	Aorta	Aorta
20	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
21	chr17:60111000-60118400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:60111000-60120200	Weak transcription	Ovary	ovary
23	chr17:60111000-60130600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:60111000-60133800	Weak transcription	Pancreas	Pancrea
25	chr17:60111200-60120200	Weak transcription	Brain Anterior Caudate	brain
26	chr17:60111200-60122600	Weak transcription	HMEC	breast
27	chr17:60111200-60123600	Weak transcription	Brain Hippocampus Middle	brain
28	chr17:60111200-60129000	Weak transcription	Brain Angular Gyrus	brain
29	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:60111400-60119800	Weak transcription	Primary T cells from cord blood	blood
31	chr17:60111400-60119800	Weak transcription	Fetal Lung	lung
32	chr17:60111400-60122200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:60111400-60122600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr17:60111400-60123000	Weak transcription	Colon Smooth Muscle	Colon
35	chr17:60111400-60123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr17:60111400-60123800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:60111400-60123800	Weak transcription	Brain Substantia Nigra	brain
38	chr17:60111400-60124600	Weak transcription	NHLF	lung
39	chr17:60111400-60128200	Weak transcription	NHEK	skin
40	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain
41	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr17:60111600-60118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:60111600-60122600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr17:60111600-60125600	Weak transcription	Fetal Kidney	kidney
46	chr17:60111600-60126200	Weak transcription	NH-A	brain
47	chr17:60112600-60120200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:60112800-60120000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr17:60112800-60122400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:60113000-60118800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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