Variant report

Variant	rs557988118
Chromosome Location	chr5:40832911-40832912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40824786-40836349	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
3	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
4	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
5	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
6	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:40832742-40836593	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr5:40826353-40836595	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:40825968-40836481	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:40824347-40836356	U87	brain:	n/a	n/a
12	POLR2A	chr5:40824803-40836847	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr5:40823660-40836653	GM12891	blood:	n/a	n/a
14	POLR2A	chr5:40832876-40836815	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:40831114-40836017	SK-N-SH	brain:	n/a	n/a
16	CHD1	chr5:40832389-40832927	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBL1XR1	chr5:40832689-40835759	K562	blood:	n/a	n/a
18	POLR2A	chr5:40824850-40836220	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr5:40824593-40835864	A549	lung:	n/a	n/a
20	POLR2A	chr5:40824520-40832990	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr5:40824315-40837212	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr5:40832768-40833429	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr5:40824609-40836766	K562	blood:	n/a	n/a
24	POLR2A	chr5:40826435-40836578	K562	blood:	n/a	n/a
25	POLR2A	chr5:40824401-40836560	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:40824471-40836545	K562	blood:	n/a	n/a
27	POLR2A	chr5:40824568-40836218	GM12892	blood:	n/a	n/a
28	POLR2A	chr5:40826481-40836754	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:40832747-40833771	HCT-116	colon:	n/a	n/a
30	POLR2A	chr5:40823728-40837176	GM12878	blood:	n/a	n/a
31	POLR2A	chr5:40824499-40835871	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:40832762-40833005	MCF-7	breast:	n/a	n/a
33	POLR2A	chr5:40824606-40836645	K562	blood:	n/a	n/a
34	TBL1XR1	chr5:40832703-40836382	K562	blood:	n/a	n/a
35	CCNT2	chr5:40832804-40833440	K562	blood:	n/a	n/a
36	KAP1	chr5:40832863-40833269	K562	blood:	n/a	n/a
37	POLR2A	chr5:40824291-40836260	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr5:40831598-40833032	HL-60	blood:	n/a	n/a
39	POLR2A	chr5:40823526-40837257	K562	blood:	n/a	n/a
40	POLR2A	chr5:40829914-40835885	HepG2	liver:	n/a	n/a
41	ZNF274	chr5:40831453-40833139	K562	blood:	n/a	n/a
42	POLR2A	chr5:40824511-40836576	GM18505	blood:	n/a	n/a
43	POLR2A	chr5:40824320-40836336	U87	brain:	n/a	n/a
44	POLR2A	chr5:40824536-40836095	HepG2	liver:	n/a	n/a
45	POLR2A	chr5:40830723-40836594	GM19099	blood:	n/a	n/a
46	POLR2A	chr5:40832697-40833346	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr5:40831779-40835811	U87	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149900207..149902355-chr5:40832606..40834765,2	MCF-7	breast:
2	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
3	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
4	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
5	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
6	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:

No data

Variant related genes	Relation type
RPL37	TF binding region
SNORD72	TF binding region
ENSG00000212567	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000143368	Chromatin interaction
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv518711	chr5:40827307-40835627	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	137 gene(s)	inside rSNPs	diseases
4	nsv968907	chr5:40832497-40834810	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 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	chr5:40823600-40833200	Strong transcription	Thymus	Thymus
2	chr5:40824200-40833000	Weak transcription	Fetal Heart	heart
3	chr5:40824200-40833000	Weak transcription	Psoas Muscle	Psoas
4	chr5:40824800-40833000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:40824800-40833200	Strong transcription	Fetal Thymus	thymus
6	chr5:40824800-40833600	Strong transcription	Brain Germinal Matrix	brain
7	chr5:40825200-40833200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:40825200-40833400	Strong transcription	Brain Anterior Caudate	brain
9	chr5:40825400-40833800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr5:40825600-40833000	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr5:40825600-40833200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:40825600-40833200	Strong transcription	Fetal Muscle Leg	muscle
13	chr5:40825600-40833200	Strong transcription	Left Ventricle	heart
14	chr5:40825600-40833400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:40825600-40833400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr5:40825800-40833200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr5:40826000-40833200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:40826000-40833200	Strong transcription	Fetal Brain Female	brain
19	chr5:40826000-40833400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr5:40826000-40833400	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr5:40826200-40833000	Strong transcription	Adipose Nuclei	Adipose
22	chr5:40826400-40833000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:40826400-40833200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr5:40826400-40833400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr5:40826600-40833000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:40826600-40833000	Strong transcription	Rectal Smooth Muscle	rectum
27	chr5:40826600-40833200	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr5:40826600-40833200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr5:40826600-40833200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:40826600-40833200	Strong transcription	Fetal Intestine Large	intestine
31	chr5:40826600-40833400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:40826600-40833600	Strong transcription	Placenta	Placenta
33	chr5:40826600-40833800	Strong transcription	Lung	lung
34	chr5:40826800-40833200	Strong transcription	Brain Angular Gyrus	brain
35	chr5:40826800-40833200	Strong transcription	Brain Hippocampus Middle	brain
36	chr5:40826800-40833200	Strong transcription	Fetal Kidney	kidney
37	chr5:40826800-40833200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr5:40826800-40833400	Strong transcription	Esophagus	oesophagus
39	chr5:40826800-40833400	Strong transcription	Ovary	ovary
40	chr5:40827000-40833200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:40827000-40833200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:40827200-40833200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:40827200-40833200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:40827400-40833400	Strong transcription	Brain Substantia Nigra	brain
45	chr5:40827600-40833600	Strong transcription	Colon Smooth Muscle	Colon
46	chr5:40828400-40833200	Weak transcription	Right Atrium	heart
47	chr5:40828800-40833200	Strong transcription	Right Ventricle	heart
48	chr5:40828800-40833600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:40830200-40834800	Transcr. at gene 5' and 3'	Hela-S3	cervix
50	chr5:40830800-40833600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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