Variant report

Variant	rs4968468
Chromosome Location	chr17:60136647-60136648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60131533..60136089-chr17:60136212..60137998,4	MCF-7	breast:
2	chr17:60108114..60110987-chr17:60135242..60137203,2	K562	blood:
3	chr17:60020965..60024852-chr17:60134621..60138471,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12450560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451910	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12600909	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs12604037	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945756	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945759	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];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945801	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];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271576	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2278812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs28654524	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3744434	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs3809753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3826419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4410139	0.81[EUR][1000 genomes]
rs4422036	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4968455	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968456	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968457	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs4968460	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4968461	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4968462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968463	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968476	0.90[CEU][hapmap]
rs57137451	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57746689	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57918684	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58241345	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58335059	0.92[ASN][1000 genomes]
rs60053512	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61469058	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61658218	0.81[EUR][1000 genomes]
rs6504084	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap]
rs7218724	1.00[ASW][hapmap];1.00[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];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221089	1.00[ASW][hapmap];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72843781	0.85[ASN][1000 genomes]
rs73336436	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs8081917	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs9630736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4968468	MED13	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
2	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:60108000-60141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:60108800-60139000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:60109000-60141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:60110600-60139800	Weak transcription	Spleen	Spleen
8	chr17:60111200-60140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:60111400-60138400	Weak transcription	Fetal Brain Male	brain
10	chr17:60111400-60140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:60111400-60141400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr17:60115000-60140000	Weak transcription	Gastric	stomach
13	chr17:60116000-60139800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:60116200-60139800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:60116600-60139000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr17:60117200-60136800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr17:60117400-60139200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:60119800-60136800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr17:60120600-60136800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:60121600-60136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:60124000-60136800	Weak transcription	Fetal Heart	heart
22	chr17:60124200-60139200	Weak transcription	Right Ventricle	heart
23	chr17:60126200-60141600	Weak transcription	Esophagus	oesophagus
24	chr17:60129400-60136800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:60129600-60139000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr17:60129800-60139000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:60129800-60139000	Weak transcription	Fetal Kidney	kidney
28	chr17:60130000-60136800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:60130000-60139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:60130400-60136800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:60130600-60139200	Weak transcription	HUVEC	blood vessel
32	chr17:60131200-60138000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:60132200-60137000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:60132400-60138800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:60133000-60136800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr17:60133000-60137000	Strong transcription	Primary B cells from cord blood	blood
37	chr17:60133200-60136800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:60133200-60136800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:60133200-60137000	Strong transcription	K562	blood
40	chr17:60133200-60137600	Weak transcription	Lung	lung
41	chr17:60133400-60136800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:60133400-60136800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:60133400-60137800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:60133600-60136800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:60133600-60140200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr17:60133800-60137200	Enhancers	Colon Smooth Muscle	Colon
47	chr17:60133800-60137200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
48	chr17:60133800-60140000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr17:60133800-60140000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr17:60134000-60136800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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