Variant report

Variant	rs4930702
Chromosome Location	chr11:64089874-64089875
allele	C/T
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	ELF1	chr11:64089756-64090243	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:64089583-64091382	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:64089779-64091538	K562	blood:	n/a	n/a
4	POLR2A	chr11:64089592-64090082	HepG2	liver:	n/a	n/a
5	ZKSCAN1	chr11:64089740-64090047	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64088399..64090085-chr11:64108067..64109781,2	K562	blood:
2	chr11:64088256..64090312-chr11:64092623..64094945,2	MCF-7	breast:
3	chr11:64087466..64090452-chr11:64106941..64109054,2	MCF-7	breast:
4	chr11:64059173..64060678-chr11:64089016..64091569,2	MCF-7	breast:

Variant related genes	Relation type
TRMT112	TF binding region
ENSG00000257069	Chromatin interaction
ENSG00000182450	Chromatin interaction
ENSG00000168071	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10792429	1.00[CEU][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11231735	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs11231742	0.83[ASN][1000 genomes]
rs11231745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231748	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs2302263	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs34499953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751117	0.82[JPT][hapmap]
rs3782101	0.87[LWK][hapmap]
rs3903175	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6591843	0.87[LWK][hapmap]
rs7107446	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73502335	0.83[AFR][1000 genomes]
rs953778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9988817	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988874	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
6	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
8	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
10	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
11	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
12	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
13	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
14	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
15	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
16	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
17	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
18	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
19	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
20	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4930702	TRMT112	cis	parietal	SCAN
rs4930702	ANKRD13D	cis	parietal	SCAN
rs4930702	BATF2	cis	cerebellum	SCAN
rs4930702	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs4930702	HSPC152	Cis_1M	lymphoblastoid	RTeQTL
rs4930702	CCDC88B	cis	cerebellum	SCAN
rs4930702	ZDHHC24	cis	parietal	SCAN
rs4930702	FADS2	cis	cerebellum	SCAN
rs4930702	CTSW	cis	cerebellum	SCAN
rs4930702	ROM1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64086200-64090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64086800-64096600	Weak transcription	Right Atrium	heart
3	chr11:64086800-64099000	Weak transcription	Small Intestine	intestine
4	chr11:64087000-64091000	Genic enhancers	Fetal Intestine Small	intestine
5	chr11:64087000-64091400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:64087000-64091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:64087000-64097200	Weak transcription	HSMMtube	muscle
8	chr11:64087000-64099000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:64087000-64099000	Weak transcription	HSMM	muscle
10	chr11:64087000-64108200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:64087200-64090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:64087200-64090400	Weak transcription	Primary B cells from cord blood	blood
13	chr11:64087200-64091400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr11:64087200-64091400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr11:64087200-64091600	Strong transcription	Fetal Muscle Leg	muscle
16	chr11:64087200-64091600	Strong transcription	Fetal Stomach	stomach
17	chr11:64087200-64098800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:64087200-64099000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:64087200-64099000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:64087400-64090000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:64087400-64090000	Weak transcription	Fetal Brain Male	brain
22	chr11:64087400-64090200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:64087400-64090200	Strong transcription	Spleen	Spleen
24	chr11:64087400-64090400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:64087400-64090600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:64087400-64091000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:64087400-64091000	Genic enhancers	HMEC	breast
28	chr11:64087400-64091200	Strong transcription	Adipose Nuclei	Adipose
29	chr11:64087400-64091600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:64087400-64093200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:64087400-64096800	Weak transcription	Psoas Muscle	Psoas
32	chr11:64087400-64097000	Weak transcription	HUVEC	blood vessel
33	chr11:64087400-64099000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:64087400-64099000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:64087600-64090000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:64087600-64090600	Strong transcription	Left Ventricle	heart
37	chr11:64087600-64091600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr11:64087800-64090600	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:64087800-64090800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:64087800-64090800	Strong transcription	Liver	Liver
41	chr11:64087800-64090800	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:64087800-64091000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:64087800-64091000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:64087800-64091200	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr11:64088000-64090200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:64088000-64090400	Strong transcription	Osteobl	bone
47	chr11:64088000-64090600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:64088000-64090800	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr11:64088000-64090800	Genic enhancers	Fetal Intestine Large	intestine
50	chr11:64088000-64090800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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