Variant report

Variant	rs4930685
Chromosome Location	chr11:64629720-64629721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64629387-64634963	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:64629559-64634892	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:64629711-64631304	U87	brain:	n/a	n/a
4	POLR2A	chr11:64615614-64641325	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:64628429-64635030	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:64629711-64634024	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64628928..64631911-chr11:64900094..64902138,2	MCF-7	breast:

Variant related genes	Relation type
EHD1	TF binding region
ENSG00000162298	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10897533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1211284	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573	0.82[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs12801172	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17146413	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2007521	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2077026	0.92[ASN][1000 genomes]
rs3741391	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3893108	1.00[ASN][1000 genomes]
rs3936999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3937000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41381745	0.96[ASN][1000 genomes]
rs4930280	0.99[ASN][1000 genomes]
rs4930281	1.00[ASN][1000 genomes]
rs57851864	0.94[ASN][1000 genomes]
rs589556	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs602347	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs607569	1.00[ASN][1000 genomes]
rs620066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs621608	0.92[ASN][1000 genomes]
rs622611	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs635722	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641623	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs649208	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653225	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654580	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs656982	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126744	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926812	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927560	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943238	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7944276	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7952306	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7952567	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
5	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
10	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
11	nsv870106	chr11:64610698-64640067	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4930685	RPS4Y1	trans	lymphoblastoid	seeQTL
rs4930685	EHD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64612600-64639000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:64613000-64629800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:64613000-64630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:64619200-64630200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:64619800-64632400	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr11:64620800-64630200	Weak transcription	Fetal Kidney	kidney
7	chr11:64622800-64630400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:64623000-64630000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:64623200-64629800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:64623200-64630800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:64623200-64633000	Enhancers	Primary hematopoietic stem cells	blood
12	chr11:64623400-64630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:64624200-64630600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:64624600-64629800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:64625200-64630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr11:64625400-64634200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr11:64626400-64630000	Weak transcription	NH-A	brain
18	chr11:64626400-64644800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:64626600-64631000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr11:64626800-64630000	Weak transcription	Fetal Heart	heart
21	chr11:64627200-64629800	Weak transcription	HUVEC	blood vessel
22	chr11:64627400-64629800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:64627400-64629800	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:64627400-64633000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:64627600-64629800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:64627600-64629800	Weak transcription	Brain Angular Gyrus	brain
27	chr11:64627600-64629800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:64627600-64630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:64627600-64630200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:64627600-64630600	Weak transcription	Pancreas	Pancrea
31	chr11:64627600-64630600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr11:64627600-64633200	Enhancers	Fetal Thymus	thymus
33	chr11:64627800-64629800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:64627800-64629800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:64627800-64629800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:64627800-64629800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:64627800-64629800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr11:64627800-64629800	Weak transcription	Brain Anterior Caudate	brain
39	chr11:64627800-64629800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr11:64627800-64629800	Weak transcription	Brain Germinal Matrix	brain
41	chr11:64627800-64629800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr11:64627800-64629800	Weak transcription	Fetal Brain Female	brain
43	chr11:64627800-64629800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:64627800-64629800	Enhancers	Stomach Smooth Muscle	stomach
45	chr11:64627800-64629800	Weak transcription	HSMMtube	muscle
46	chr11:64627800-64629800	Weak transcription	NHEK	skin
47	chr11:64627800-64629800	Weak transcription	Osteobl	bone
48	chr11:64627800-64630000	Weak transcription	Stomach Mucosa	stomach
49	chr11:64627800-64630000	Weak transcription	HMEC	breast
50	chr11:64627800-64630400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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