Variant report

Variant	rs7948729
Chromosome Location	chr11:5705625-5705626
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	RELA	chr11:5705574-5706758	GM10847	blood:	n/a	n/a
2	GTF2F1	chr11:5705621-5706610	Hela-S3	cervix:	n/a	n/a
3	UBTF	chr11:5705604-5706425	K562	blood:	n/a	n/a
4	CTCF	chr11:5705440-5705690	AG04450	lung:	n/a	n/a
5	POLR2A	chr11:5705579-5706739	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:5705598-5706615	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:5704924-5706864	GM15510	blood:	n/a	n/a
8	CTCF	chr11:5705321-5706844	A549	lung:	n/a	chr11:5705994-5706007
9	POLR2A	chr11:5703536-5706824	IMR90	lung:	n/a	n/a
10	TBP	chr11:5705578-5706601	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:5704925-5706866	GM12891	blood:	n/a	n/a
12	MXI1	chr11:5705426-5706640	GM12878	blood:	n/a	n/a
13	RELA	chr11:5705582-5706663	GM15510	blood:	n/a	n/a
14	MTA3	chr11:5705565-5706637	GM12878	blood:	n/a	n/a
15	USF2	chr11:5705516-5706565	GM12878	blood:	n/a	n/a
16	CHD1	chr11:5705573-5706522	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:5705538-5706733	GM12892	blood:	n/a	n/a
18	BRCA1	chr11:5705534-5706602	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr11:5705603-5706650	GM18505	blood:	n/a	n/a
20	POLR2A	chr11:5704791-5706700	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:5705560-5706671	PANC-1	pancreas:	n/a	n/a
22	JUND	chr11:5705612-5706892	SK-N-SH	brain:	n/a	chr11:5706370-5706378
23	POLR2A	chr11:5704949-5706674	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr11:5704925-5706532	PBDE	blood:	n/a	n/a
25	SIN3AK20	chr11:5705520-5706299	PANC-1	pancreas:	n/a	n/a
26	EP300	chr11:5705528-5706472	GM12878	blood:	n/a	n/a
27	SIN3A	chr11:5705527-5706505	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr11:5705476-5706558	GM12878	blood:	n/a	n/a
29	STAT5A	chr11:5705610-5706490	GM12878	blood:	n/a	chr11:5705896-5705908 chr11:5706124-5706131 chr11:5706270-5706278 chr11:5706322-5706333
30	RELA	chr11:5705503-5706631	GM12891	blood:	n/a	n/a
31	WRNIP1	chr11:5705318-5706572	GM12878	blood:	n/a	n/a
32	NR2F2	chr11:5705604-5706477	K562	blood:	n/a	n/a
33	POLR2A	chr11:5705377-5706744	HUVEC	blood vessel:	n/a	n/a
34	MAZ	chr11:5705556-5706537	GM12878	blood:	n/a	n/a
35	RFX5	chr11:5705579-5706611	Hela-S3	cervix:	n/a	chr11:5706428-5706445
36	RELA	chr11:5705566-5706505	GM18951	blood:	n/a	n/a
37	POLR2A	chr11:5705603-5705789	GM12878	blood:	n/a	n/a
38	POU2F2	chr11:5704872-5706595	GM12878	blood:	n/a	n/a
39	POLR2A	chr11:5704753-5706635	GM12878	blood:	n/a	n/a
40	BHLHE40	chr11:5705615-5706560	K562	blood:	n/a	n/a
41	POLR2A	chr11:5704926-5706625	GM12892	blood:	n/a	n/a
42	POLR2A	chr11:5705370-5706669	GM19099	blood:	n/a	n/a
43	POLR2A	chr11:5704925-5706840	GM12878	blood:	n/a	n/a
44	FOXM1	chr11:5705583-5706514	GM12878	blood:	n/a	chr11:5706457-5706465
45	CEBPB	chr11:5705506-5706822	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5523660..5528079-chr11:5704615..5707879,4	K562	blood:
2	chr11:5700658..5702927-chr11:5704276..5706133,2	K562	blood:
3	11:5033143-5038367..11:5700314-5707362	K562	blood:
4	11:4801044-4820112..11:5700314-5707362	H1-hESC	embryonic stem cell:	embryo
5	11:4988858-5002113..11:5700314-5707362	Hela-S3	cervix:
6	chr11:5524818..5527723-chr11:5704615..5707499,2	K562	blood:

Variant related genes	Relation type
TRIM5	TF binding region
ENSG00000213931	Chromatin interaction
ENSG00000231070	Chromatin interaction
ENSG00000176951	Chromatin interaction
ENSG00000196565	Chromatin interaction
ENSG00000132256	Chromatin interaction
ENSG00000225003	Chromatin interaction
ENSG00000167355	Chromatin interaction
ENSG00000224300	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs61639923	1.00[AFR][1000 genomes]
rs7935494	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5701400-5705800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:5704600-5705800	Active TSS	Dnd41	blood
3	chr11:5704600-5706600	Active TSS	Colonic Mucosa	Colon
4	chr11:5704600-5706800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:5704600-5706800	Active TSS	Stomach Smooth Muscle	stomach
6	chr11:5704800-5706600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr11:5705000-5706400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:5705000-5706400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:5705000-5706400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:5705000-5706400	Active TSS	Colon Smooth Muscle	Colon
11	chr11:5705000-5706400	Active TSS	Fetal Lung	lung
12	chr11:5705000-5706400	Active TSS	Pancreas	Pancrea
13	chr11:5705000-5706400	Active TSS	NHLF	lung
14	chr11:5705000-5706600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr11:5705000-5706600	Active TSS	Fetal Intestine Small	intestine
16	chr11:5705000-5706600	Active TSS	Thymus	Thymus
17	chr11:5705000-5706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:5705000-5706800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr11:5705200-5705800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:5705200-5705800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr11:5705200-5705800	Flanking Active TSS	Fetal Thymus	thymus
22	chr11:5705200-5706000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr11:5705200-5706000	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr11:5705200-5706000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr11:5705200-5706000	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr11:5705200-5706000	Flanking Active TSS	HUVEC	blood vessel
27	chr11:5705200-5706200	Active TSS	Fetal Muscle Trunk	muscle
28	chr11:5705200-5706400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:5705200-5706400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:5705200-5706400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:5705200-5706400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:5705200-5706400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:5705200-5706400	Active TSS	Fetal Intestine Large	intestine
34	chr11:5705200-5706400	Active TSS	Lung	lung
35	chr11:5705200-5706400	Active TSS	Right Ventricle	heart
36	chr11:5705200-5706400	Active TSS	HSMM	muscle
37	chr11:5705200-5706600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:5705200-5706600	Active TSS	Liver	Liver
39	chr11:5705200-5706600	Active TSS	Brain Angular Gyrus	brain
40	chr11:5705200-5706600	Active TSS	Fetal Stomach	stomach
41	chr11:5705200-5706600	Active TSS	Small Intestine	intestine
42	chr11:5705200-5706600	Active TSS	A549	lung
43	chr11:5705200-5706800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:5705200-5706800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr11:5705200-5706800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr11:5705200-5706800	Active TSS	GM12878-XiMat	blood
47	chr11:5705400-5705800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr11:5705400-5705800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr11:5705400-5705800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:5705400-5705800	Flanking Active TSS	Primary T cells from cord blood	blood

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