Variant report

Variant	rs11100583
Chromosome Location	chr4:165877645-165877646
allele	C/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	chr4:165877518-165880399	MCF10A-Er-Src	breast:	n/a	n/a
2	GABPA	chr4:165877606-165878746	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165868972..165872041-chr4:165876298..165879460,3	MCF-7	breast:
2	chr4:165876074..165878048-chr4:165892405..165894471,2	MCF-7	breast:

Variant related genes	Relation type
FAM218A	TF binding region
ENSG00000236941	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11942693	0.90[CHB][hapmap]
rs11942750	0.90[CHB][hapmap]
rs12507869	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510464	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12512234	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12647427	0.89[CHB][hapmap]
rs13110309	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13120990	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs13134940	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13137799	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs13140290	0.82[ASN][1000 genomes]
rs13144590	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13151290	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13151735	0.85[CHB][hapmap]
rs1401401	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs17623445	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733418	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733419	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4234889	0.85[ASN][1000 genomes]
rs4395461	0.85[ASN][1000 genomes]
rs4690797	0.84[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4691138	0.84[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61641856	0.85[ASN][1000 genomes]
rs6834073	0.85[ASN][1000 genomes]
rs71641138	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72697952	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7656863	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657444	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657639	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv517554	chr4:165859951-165878335	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
15	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	esv3692850	chr4:165868229-165879381	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	esv2421831	chr4:165868229-165882293	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165871000-165877800	Weak transcription	Spleen	Spleen
2	chr4:165874000-165877800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:165874000-165878000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:165874200-165877800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:165875600-165877800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:165875600-165877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:165877000-165877800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:165877200-165877800	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:165877200-165877800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr4:165877200-165877800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:165877200-165877800	Enhancers	Pancreas	Pancrea
12	chr4:165877200-165879000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr4:165877400-165877800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr4:165877400-165877800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr4:165877400-165877800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:165877400-165877800	Enhancers	Brain Anterior Caudate	brain
17	chr4:165877400-165877800	Enhancers	Lung	lung
18	chr4:165877400-165877800	Enhancers	Ovary	ovary
19	chr4:165877400-165878800	Active TSS	Primary T cells from cord blood	blood
20	chr4:165877400-165879000	Active TSS	Stomach Smooth Muscle	stomach
21	chr4:165877600-165877800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr4:165877600-165877800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:165877600-165877800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:165877600-165877800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr4:165877600-165877800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr4:165877600-165877800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr4:165877600-165877800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:165877600-165877800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:165877600-165877800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:165877600-165877800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr4:165877600-165877800	Active TSS	Adipose Nuclei	Adipose
32	chr4:165877600-165877800	Active TSS	Duodenum Mucosa	Duodenum
33	chr4:165877600-165877800	Enhancers	Fetal Heart	heart
34	chr4:165877600-165877800	Active TSS	Fetal Muscle Trunk	muscle
35	chr4:165877600-165877800	Active TSS	Placenta	Placenta
36	chr4:165877600-165877800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr4:165877600-165877800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr4:165877600-165877800	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr4:165877600-165877800	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:165877600-165877800	Active TSS	HUVEC	blood vessel
41	chr4:165877600-165877800	Enhancers	NHEK	skin
42	chr4:165877600-165877800	Enhancers	Osteobl	bone
43	chr4:165877600-165878000	Active TSS	Right Atrium	heart
44	chr4:165877600-165878400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:165877600-165878400	Active TSS	Fetal Stomach	stomach
46	chr4:165877600-165878600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr4:165877600-165878600	Active TSS	Colon Smooth Muscle	Colon
48	chr4:165877600-165878800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr4:165877600-165878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:165877600-165878800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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