Variant report

Variant	rs29762
Chromosome Location	chr5:40833274-40833275
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

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	chr5:40833076-40833392	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
4	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
5	POLR2A	chr5:40833177-40833368	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
7	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
8	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
9	IRF1	chr5:40833040-40835975	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
10	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:40833129-40836609	GM12878	blood:	n/a	n/a
12	WRNIP1	chr5:40833235-40836410	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:40832988-40835995	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:40832742-40836593	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr5:40826353-40836595	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:40825968-40836481	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:40824347-40836356	U87	brain:	n/a	n/a
18	POLR2A	chr5:40833106-40836648	K562	blood:	n/a	n/a
19	POLR2A	chr5:40833006-40836182	MCF-7	breast:	n/a	n/a
20	POLR2A	chr5:40824803-40836847	Hela-S3	cervix:	n/a	n/a
21	HEY1	chr5:40833081-40836488	K562	blood:	n/a	n/a
22	POLR2A	chr5:40833227-40833541	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:40833161-40833540	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr5:40833210-40836619	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr5:40833039-40836469	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr5:40823660-40836653	GM12891	blood:	n/a	n/a
27	POLR2A	chr5:40832876-40836815	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr5:40831114-40836017	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr5:40832989-40836520	PANC-1	pancreas:	n/a	n/a
30	TBL1XR1	chr5:40832689-40835759	K562	blood:	n/a	n/a
31	POLR2A	chr5:40833109-40833816	GM12891	blood:	n/a	n/a
32	POLR2A	chr5:40833168-40836438	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr5:40824850-40836220	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr5:40824593-40835864	A549	lung:	n/a	n/a
35	MYC	chr5:40833202-40836510	K562	blood:	n/a	chr5:40833644-40833653
36	POLR2A	chr5:40824315-40837212	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr5:40832768-40833429	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr5:40824609-40836766	K562	blood:	n/a	n/a
39	POLR2A	chr5:40826435-40836578	K562	blood:	n/a	n/a
40	CHD1	chr5:40833188-40833335	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:40833166-40836558	K562	blood:	n/a	n/a
42	POLR2A	chr5:40824401-40836560	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr5:40833106-40836499	HL-60	blood:	n/a	n/a
44	POLR2A	chr5:40824471-40836545	K562	blood:	n/a	n/a
45	POLR2A	chr5:40833106-40836043	GM12892	blood:	n/a	n/a
46	POLR2A	chr5:40824568-40836218	GM12892	blood:	n/a	n/a
47	POLR2A	chr5:40826481-40836754	HepG2	liver:	n/a	n/a
48	HEY1	chr5:40833203-40833455	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:40833046-40833588	GM12891	blood:	n/a	n/a
50	POLR2A	chr5:40833175-40833337	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:40833236-40833286	MCF-7	breast:	n/a
2	chr5:40833236-40833286	AG09319	gingival:	n/a
3	chr5:40833236-40833286	SK-N-SH_RA	brain:	n/a
4	chr5:40833236-40833286	HAEpiC	amniotic membrane:	n/a
5	chr5:40833236-40833286	HIPEpiC	eye:	n/a
6	chr5:40833236-40833286	HL-60	blood:	n/a
7	chr5:40833236-40833286	GM19239	blood:	n/a
8	chr5:40833236-40833286	GM06990	blood:	n/a
9	chr5:40833236-40833286	SK-N-SH	brain:	n/a
10	chr5:40833236-40833286	HRPEpiC	eye:	n/a
11	chr5:40833236-40833286	Hela-S3	cervix:	n/a
12	chr5:40833236-40833286	K562	blood:	n/a
13	chr5:40833236-40833286	HEK293	kidney:	embryo
14	chr5:40833236-40833286	NH-A	brain:	n/a
15	chr5:40833236-40833286	NHDF-neo	bronchial:	n/a
16	chr5:40833236-40833286	HUVEC	blood vessel:	n/a
17	chr5:40833236-40833286	Hepatocyte	liver:	n/a
18	chr5:40833236-40833286	BJ	skin:	n/a
19	chr5:40833236-40833286	T-47D	breast:	n/a
20	chr5:40833236-40833286	HCF	heart:	n/a
21	chr5:40833236-40833286	PrEC	prostate:	n/a
22	chr5:40833236-40833286	AG09309	skin:	n/a
23	chr5:40833236-40833286	GM12878	blood:	n/a
24	chr5:40833236-40833286	MCF10A-Er-Src	breast:	n/a
25	chr5:40833236-40833286	SKMC	muscle:	n/a
26	chr5:40833236-40833286	ECC-1	luminal epithelium:	n/a
27	chr5:40833236-40833286	A549	lung:	n/a
28	chr5:40833236-40833286	PANC-1	pancreas:	n/a
29	chr5:40833236-40833286	HEEpiC	esophagus:	n/a
30	chr5:40833236-40833286	ovcar-3	ovarian:	n/a
31	chr5:40833236-40833286	RPTEC	kidney:	n/a
32	chr5:40833236-40833286	NT2-D1	testis:	n/a
33	chr5:40833236-40833286	NB4	blood:	n/a
34	chr5:40833236-40833286	H1-hESC	embryonic stem cell:	embryo
35	chr5:40833236-40833286	AG10803	skin:	n/a
36	chr5:40833236-40833286	HepG2	liver:	n/a
37	chr5:40833236-40833286	HPAEpiC	pulmonary alveolar:	n/a
38	chr5:40833236-40833286	SK-N-MC	brain:	n/a
39	chr5:40833236-40833286	HCT-116	colon:	n/a
40	chr5:40833236-40833286	Jurkat	blood:	n/a
41	chr5:40833236-40833286	BE2_C	brain:	n/a
42	chr5:40833236-40833286	HRE	kidney:	n/a
43	chr5:40833236-40833286	GM12891	blood:	n/a
44	chr5:40833236-40833286	HMEC	breast:	n/a
45	chr5:40833236-40833286	NHBE	bronchial:	n/a
46	chr5:40833236-40833286	PFSK-1	brain:	n/a
47	chr5:40833236-40833286	AoSMC	blood vessel:	n/a
48	chr5:40833236-40833286	Caco-2	colon:	n/a
49	chr5:40833236-40833286	HCPEpiC	choroid plexus:	n/a
50	chr5:40833236-40833286	U87	brain:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155164065..155164688-chr5:40833264..40834066,2	Hela-S3	cervix:
2	chr1:149900207..149902355-chr5:40832606..40834765,2	MCF-7	breast:
3	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
4	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
5	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
6	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
7	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
8	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
9	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
SNORD72	CpG island
RPL37	CpG island
ENSG00000113638	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000143368	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10064232	0.88[ASN][1000 genomes]
rs1070444	1.00[JPT][hapmap]
rs1070445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1097592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1097604	0.94[ASN][1000 genomes]
rs152374	1.00[JPT][hapmap]
rs1530811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs154272	0.88[ASN][1000 genomes]
rs154273	1.00[ASN][1000 genomes]
rs154274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs154276	1.00[JPT][hapmap]
rs154278	1.00[JPT][hapmap]
rs154282	1.00[JPT][hapmap]
rs154283	1.00[JPT][hapmap]
rs1631661	1.00[ASN][1000 genomes]
rs1645509	0.88[ASN][1000 genomes]
rs166282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1697929	0.94[ASN][1000 genomes]
rs1697937	0.94[ASN][1000 genomes]
rs173619	0.88[ASN][1000 genomes]
rs181819	0.82[ASN][1000 genomes]
rs181820	0.88[ASN][1000 genomes]
rs181821	0.88[ASN][1000 genomes]
rs1833892	0.88[ASN][1000 genomes]
rs184436	0.94[ASN][1000 genomes]
rs187274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs192962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2262009	0.94[ASN][1000 genomes]
rs249408	0.81[ASN][1000 genomes]
rs249409	0.81[ASN][1000 genomes]
rs249411	0.81[ASN][1000 genomes]
rs249412	0.81[ASN][1000 genomes]
rs249439	0.88[ASN][1000 genomes]
rs249443	1.00[ASN][1000 genomes]
rs249444	1.00[ASN][1000 genomes]
rs29737	1.00[JPT][hapmap]
rs29763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs29764	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs323554	0.88[ASN][1000 genomes]
rs323556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs323560	0.94[ASN][1000 genomes]
rs323562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34236150	0.88[ASN][1000 genomes]
rs370346	0.88[ASN][1000 genomes]
rs396412	0.88[ASN][1000 genomes]
rs39794	1.00[ASN][1000 genomes]
rs408238	0.88[ASN][1000 genomes]
rs4129381	0.81[ASN][1000 genomes]
rs418494	0.94[ASN][1000 genomes]
rs424787	0.88[ASN][1000 genomes]
rs42515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs433730	0.94[ASN][1000 genomes]
rs438604	0.88[ASN][1000 genomes]
rs441016	0.88[ASN][1000 genomes]
rs442869	0.88[ASN][1000 genomes]
rs445367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs455374	0.88[ASN][1000 genomes]
rs455519	1.00[JPT][hapmap]
rs457111	0.88[ASN][1000 genomes]
rs458884	0.88[ASN][1000 genomes]
rs459491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs459794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs460752	0.88[ASN][1000 genomes]
rs463040	0.88[ASN][1000 genomes]
rs463675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs463905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs464045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs464191	0.88[ASN][1000 genomes]
rs465467	0.88[ASN][1000 genomes]
rs466960	1.00[ASN][1000 genomes]
rs467438	0.88[ASN][1000 genomes]
rs694217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs704034	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7717507	0.88[ASN][1000 genomes]
rs837102	1.00[JPT][hapmap]
rs837119	0.81[ASN][1000 genomes]
rs837378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs837381	0.94[ASN][1000 genomes]
rs837382	0.94[ASN][1000 genomes]
rs837384	0.94[ASN][1000 genomes]
rs837385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs837389	0.94[ASN][1000 genomes]

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	chr5:40824800-40833600	Strong transcription	Brain Germinal Matrix	brain
2	chr5:40825200-40833400	Strong transcription	Brain Anterior Caudate	brain
3	chr5:40825400-40833800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:40825600-40833400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:40825600-40833400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr5:40826000-40833400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:40826000-40833400	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr5:40826400-40833400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr5:40826600-40833400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:40826600-40833600	Strong transcription	Placenta	Placenta
11	chr5:40826600-40833800	Strong transcription	Lung	lung
12	chr5:40826800-40833400	Strong transcription	Esophagus	oesophagus
13	chr5:40826800-40833400	Strong transcription	Ovary	ovary
14	chr5:40827400-40833400	Strong transcription	Brain Substantia Nigra	brain
15	chr5:40827600-40833600	Strong transcription	Colon Smooth Muscle	Colon
16	chr5:40828800-40833600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:40830200-40834800	Transcr. at gene 5' and 3'	Hela-S3	cervix
18	chr5:40830800-40833600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:40831200-40834400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr5:40831400-40833600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:40831400-40834600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:40831400-40835000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:40831600-40833400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:40831600-40835000	Transcr. at gene 5' and 3'	K562	blood
25	chr5:40831800-40833600	Genic enhancers	Stomach Mucosa	stomach
26	chr5:40831800-40834800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
27	chr5:40831800-40835000	Transcr. at gene 5' and 3'	A549	lung
28	chr5:40831800-40835200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr5:40832000-40833800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr5:40832000-40835000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
31	chr5:40832000-40835200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
32	chr5:40832200-40833600	Genic enhancers	Liver	Liver
33	chr5:40832200-40833800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:40832200-40834600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
37	chr5:40832200-40834600	Transcr. at gene 5' and 3'	NH-A	brain
38	chr5:40832200-40835000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
39	chr5:40832200-40835000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
40	chr5:40832400-40833400	Weak transcription	Fetal Brain Male	brain
41	chr5:40832400-40834000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr5:40832400-40834800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
43	chr5:40832600-40833400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:40832600-40834000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr5:40832600-40834000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:40832600-40834400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr5:40832600-40834400	Transcr. at gene 5' and 3'	HepG2	liver
48	chr5:40832600-40834400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
49	chr5:40832600-40834600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
50	chr5:40832600-40834600	Transcr. at gene 5' and 3'	HMEC	breast

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