Variant report

Variant	rs939108
Chromosome Location	chr11:45936817-45936818
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	chr11:45936108-45936861	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:45935550-45937683	K562	blood:	n/a	n/a
3	POLR2A	chr11:45936566-45936936	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:45935386-45937340	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:45935693-45937369	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:45936304-45936930	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:45934656-45936909	GM12892	blood:	n/a	n/a
8	POLR2A	chr11:45936771-45937120	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:45934917-45936866	K562	blood:	n/a	n/a

Variant related genes	Relation type
PEX16	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10838530	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10838531	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11038706	0.80[ASN][1000 genomes]
rs1132349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2271847	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2280331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3802758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109981	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124323	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7124434	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7925824	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs867813	0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1807609	chr11:45915859-45940195	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv1798496	chr11:45925495-45948304	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45922600-45938400	Weak transcription	Fetal Kidney	kidney
2	chr11:45923000-45938000	Weak transcription	NHDF-Ad	bronchial
3	chr11:45923000-45938400	Weak transcription	Right Atrium	heart
4	chr11:45927200-45937600	Weak transcription	Stomach Mucosa	stomach
5	chr11:45928000-45937800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:45929800-45938000	Strong transcription	Fetal Intestine Small	intestine
7	chr11:45930000-45937400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:45930200-45937000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:45930200-45937200	Strong transcription	Thymus	Thymus
10	chr11:45930400-45937600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:45930400-45937600	Strong transcription	Fetal Stomach	stomach
12	chr11:45930400-45937800	Strong transcription	Fetal Intestine Large	intestine
13	chr11:45930400-45938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:45930400-45938000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:45930400-45938000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:45930400-45938000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:45930400-45938000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:45930600-45937000	Strong transcription	Lung	lung
19	chr11:45930600-45937200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:45930600-45937400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:45930600-45937600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:45930600-45937600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:45930600-45937600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:45930600-45937600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:45930600-45937600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:45930600-45937800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:45930600-45937800	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr11:45930600-45937800	Strong transcription	Placenta	Placenta
29	chr11:45930600-45937800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr11:45930600-45937800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr11:45930600-45938000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:45930600-45938000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr11:45930600-45938000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:45930600-45938000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:45930800-45937000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:45930800-45937000	Strong transcription	Brain Hippocampus Middle	brain
37	chr11:45930800-45937000	Strong transcription	Esophagus	oesophagus
38	chr11:45930800-45937200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:45930800-45937400	Strong transcription	Colonic Mucosa	Colon
40	chr11:45930800-45937600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:45930800-45937600	Strong transcription	Adipose Nuclei	Adipose
42	chr11:45930800-45937600	Strong transcription	Pancreas	Pancrea
43	chr11:45930800-45937800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:45930800-45937800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:45930800-45938000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:45930800-45938000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:45931000-45937200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr11:45931000-45937400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr11:45931000-45937600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:45931000-45937800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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