Variant report

Variant	rs11548822
Chromosome Location	chr5:40680317-40680318
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	POLR2A	chr5:40678901-40680830	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr5:40680066-40682391	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:40678244-40680457	NB4	blood:	n/a	n/a
4	MAX	chr5:40678144-40680687	NB4	blood:	n/a	n/a
5	POLR2A	chr5:40679045-40680651	MCF-7	breast:	n/a	n/a
6	TCF12	chr5:40679495-40680455	ECC-1	luminal epithelium:	n/a	chr5:40679806-40679813
7	ZNF143	chr5:40680018-40680669	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr5:40679949-40682335	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr5:40679505-40680715	H1-hESC	embryonic stem cell:	n/a	chr5:40679536-40679545
10	CHD2	chr5:40680077-40680938	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr5:40678512-40680410	U87	brain:	n/a	n/a
12	REST	chr5:40679016-40680444	HL-60	blood:	n/a	chr5:40679637-40679650 chr5:40679808-40679821
13	MAX	chr5:40679061-40680761	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr5:40679479-40680805	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZEB1	chr5:40679874-40680359	GM12878	blood:	n/a	n/a
16	CHD2	chr5:40678769-40680438	Hela-S3	cervix:	n/a	n/a
17	TFAP2C	chr5:40679017-40680425	Hela-S3	cervix:	n/a	n/a
18	MAX	chr5:40679489-40680420	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:40678546-40680369	PANC-1	pancreas:	n/a	n/a
20	ZKSCAN1	chr5:40678910-40680342	Hela-S3	cervix:	n/a	n/a
21	MAX	chr5:40678934-40680545	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr5:40678798-40680512	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:40679110-40680347	HUVEC	blood vessel:	n/a	n/a
24	MAX	chr5:40678843-40680600	A549	lung:	n/a	n/a
25	POLR2A	chr5:40678596-40680801	HL-60	blood:	n/a	n/a
26	TAF1	chr5:40679867-40680404	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr5:40679281-40680482	PFSK-1	brain:	n/a	n/a
28	SMARCC1	chr5:40678796-40680595	Hela-S3	cervix:	n/a	n/a
29	UBTF	chr5:40679624-40680443	K562	blood:	n/a	n/a
30	SIN3AK20	chr5:40679500-40680341	PANC-1	pancreas:	n/a	n/a
31	E2F6	chr5:40678968-40682262	H1-hESC	embryonic stem cell:	n/a	chr5:40679536-40679545
32	POLR2A	chr5:40677912-40680908	MCF10A-Er-Src	breast:	n/a	n/a
33	TFAP2A	chr5:40678997-40680533	Hela-S3	cervix:	n/a	chr5:40679529-40679537 chr5:40680073-40680088 chr5:40679529-40679537 chr5:40679529-40679537
34	HDAC2	chr5:40679495-40680347	MCF-7	breast:	n/a	n/a
35	POLR2A	chr5:40678223-40680323	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr5:40678513-40682518	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr5:40679114-40680395	MCF-7	breast:	n/a	n/a
38	POLR2A	chr5:40678881-40680341	PANC-1	pancreas:	n/a	n/a
39	TCF12	chr5:40679851-40680422	A549	lung:	n/a	n/a
40	STAT1	chr5:40678305-40680617	Hela-S3	cervix:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
41	POLR2A	chr5:40678573-40680352	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr5:40678769-40680678	Raji	blood:	n/a	n/a
43	POLR2A	chr5:40679828-40680319	GM12892	blood:	n/a	n/a
44	E2F6	chr5:40680008-40680559	A549	lung:	n/a	n/a
45	POLR2A	chr5:40678805-40680443	HUVEC	blood vessel:	n/a	n/a
46	REST	chr5:40679907-40680447	A549	lung:	n/a	n/a
47	RCOR1	chr5:40678649-40680348	Hela-S3	cervix:	n/a	n/a
48	SIN3A	chr5:40679995-40680810	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr5:40679022-40680339	SK-N-MC	brain:	n/a	n/a
50	TCF7L2	chr5:40680087-40680730	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:103497..104162-chr5:40679412..40680348,2	Hela-S3	cervix:
2	chr14:75746315..75746996-chr5:40679492..40680585,3	Hela-S3	cervix:
3	chr1:149223620..149224423-chr5:40679508..40680359,2	MCF-7	breast:
4	chr5:40679791..40680505-chr9:140135439..140136378,2	Hela-S3	cervix:
5	chr19:42756164..42759141-chr5:40680173..40681787,2	MCF-7	breast:
6	chr3:150480176..150481089-chr5:40680039..40680660,2	Hela-S3	cervix:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000188229	Chromatin interaction
ENSG00000161981	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000161980	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000170345	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3397684	chr5:40678645-40681143	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum
2	chr5:40677400-40681000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:40677800-40681000	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr5:40678200-40680400	Active TSS	Stomach Smooth Muscle	stomach
5	chr5:40678200-40680800	Active TSS	Dnd41	blood
6	chr5:40678400-40680800	Active TSS	A549	lung
7	chr5:40678400-40681000	Active TSS	Fetal Intestine Small	intestine
8	chr5:40678400-40681000	Active TSS	Thymus	Thymus
9	chr5:40678400-40681400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:40678400-40682000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:40678400-40683800	Active TSS	HSMM	muscle
12	chr5:40678400-40684600	Active TSS	HSMMtube	muscle
13	chr5:40678600-40680400	Active TSS	Colonic Mucosa	Colon
14	chr5:40678600-40680400	Active TSS	Right Ventricle	heart
15	chr5:40678600-40680600	Active TSS	Stomach Mucosa	stomach
16	chr5:40678600-40680800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:40678600-40681000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:40678600-40681200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:40678600-40681200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:40678600-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:40678600-40682200	Active TSS	NHEK	skin
22	chr5:40678600-40684400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr5:40678600-40685800	Active TSS	Right Atrium	heart
24	chr5:40678800-40680400	Bivalent/Poised TSS	Psoas Muscle	Psoas
25	chr5:40678800-40680600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr5:40678800-40680800	Active TSS	HMEC	breast
27	chr5:40678800-40681000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:40678800-40681000	Active TSS	NHDF-Ad	bronchial
29	chr5:40678800-40681200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:40678800-40681200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:40678800-40683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:40679000-40680400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:40679000-40680400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:40679000-40680400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr5:40679000-40680400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:40679000-40680400	Active TSS	Spleen	Spleen
37	chr5:40679000-40680600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr5:40679000-40680800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:40679000-40681000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:40679000-40681000	Active TSS	Esophagus	oesophagus
41	chr5:40679000-40681200	Active TSS	Left Ventricle	heart
42	chr5:40679000-40681200	Active TSS	Pancreas	Pancrea
43	chr5:40679000-40681200	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr5:40679000-40681400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr5:40679000-40681400	Active TSS	Gastric	stomach
46	chr5:40679000-40682000	Active TSS	Aorta	Aorta
47	chr5:40679000-40682400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:40679000-40685600	Active TSS	Colon Smooth Muscle	Colon
49	chr5:40679000-40689400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:40679200-40680400	Active TSS	Brain Anterior Caudate	brain

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