Variant report

Variant	rs29761
Chromosome Location	chr5:40833487-40833488
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 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	chr5:40833397-40836297	GM15510	blood:	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	chr5:40824383-40836719	K562	blood:	n/a	n/a
6	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
7	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
8	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
9	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:40833129-40836609	GM12878	blood:	n/a	n/a
11	WRNIP1	chr5:40833235-40836410	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:40832988-40835995	GM12892	blood:	n/a	n/a
13	POLR2A	chr5:40833376-40836533	Hela-S3	cervix:	n/a	n/a
14	USF2	chr5:40833426-40836685	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr5:40832742-40836593	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr5:40826353-40836595	GM12878	blood:	n/a	n/a
17	POLR2A	chr5:40825968-40836481	GM12878	blood:	n/a	n/a
18	SMARCB1	chr5:40833425-40836418	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:40824347-40836356	U87	brain:	n/a	n/a
20	POLR2A	chr5:40833106-40836648	K562	blood:	n/a	n/a
21	POLR2A	chr5:40833006-40836182	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:40824803-40836847	Hela-S3	cervix:	n/a	n/a
23	HEY1	chr5:40833081-40836488	K562	blood:	n/a	n/a
24	POLR2A	chr5:40833227-40833541	GM12891	blood:	n/a	n/a
25	POLR2A	chr5:40833161-40833540	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr5:40833210-40836619	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr5:40833039-40836469	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr5:40823660-40836653	GM12891	blood:	n/a	n/a
29	POLR2A	chr5:40832876-40836815	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr5:40831114-40836017	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr5:40832989-40836520	PANC-1	pancreas:	n/a	n/a
32	TBL1XR1	chr5:40832689-40835759	K562	blood:	n/a	n/a
33	POLR2A	chr5:40833109-40833816	GM12891	blood:	n/a	n/a
34	KAP1	chr5:40833480-40835606	K562	blood:	n/a	chr5:40835321-40835329
35	POLR2A	chr5:40833168-40836438	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr5:40824850-40836220	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr5:40824593-40835864	A549	lung:	n/a	n/a
38	MYC	chr5:40833202-40836510	K562	blood:	n/a	chr5:40833644-40833653
39	POLR2A	chr5:40824315-40837212	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr5:40824609-40836766	K562	blood:	n/a	n/a
41	POLR2A	chr5:40826435-40836578	K562	blood:	n/a	n/a
42	GATA3	chr5:40833455-40833835	SH-SY5Y	brain:	n/a	n/a
43	POLR2A	chr5:40833166-40836558	K562	blood:	n/a	n/a
44	POLR2A	chr5:40824401-40836560	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr5:40833106-40836499	HL-60	blood:	n/a	n/a
46	POLR2A	chr5:40824471-40836545	K562	blood:	n/a	n/a
47	POLR2A	chr5:40833106-40836043	GM12892	blood:	n/a	n/a
48	POLR2A	chr5:40824568-40836218	GM12892	blood:	n/a	n/a
49	POLR2A	chr5:40833449-40833695	HepG2	liver:	n/a	n/a
50	POLR2A	chr5:40833465-40836122	PBDE	blood:	n/a	n/a

No data

(count:10 , 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	chr5:40762484..40765387-chr5:40833487..40838148,4	K562	blood:
4	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
5	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
6	chr5:40752902..40758440-chr5:40826185..40833524,16	K562	blood:
7	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
8	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
9	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
10	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
ENSG00000113638	Chromatin interaction
ENSG00000143368	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000132356	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10060234	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs1070446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155724	0.90[CEU][hapmap]
rs13167906	0.90[CEU][hapmap]
rs154268	0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs154275	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs171605	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs173620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs249414	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs249422	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs249425	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs249428	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs249429	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap]
rs249437	0.92[ASN][1000 genomes]
rs249441	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs257009	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs29742	0.82[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs29743	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs29744	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs376831	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs381471	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389737	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434778	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs4383756	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs447810	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs457776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461404	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs462366	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466108	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6451535	0.90[JPT][hapmap]
rs6897470	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7711806	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs7726237	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs837101	0.85[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[YRI][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs29761	FBXO4	cis	parietal	SCAN
rs29761		cis	Lymphoblastoid	GTEx
rs29761	RPL37	cis	cerebellum	SCAN
rs29761	RPL37	cis	parietal	SCAN

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	chr5:40825400-40833800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr5:40826600-40833600	Strong transcription	Placenta	Placenta
4	chr5:40826600-40833800	Strong transcription	Lung	lung
5	chr5:40827600-40833600	Strong transcription	Colon Smooth Muscle	Colon
6	chr5:40828800-40833600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:40830200-40834800	Transcr. at gene 5' and 3'	Hela-S3	cervix
8	chr5:40830800-40833600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:40831200-40834400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr5:40831400-40833600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:40831400-40834600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:40831400-40835000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:40831600-40835000	Transcr. at gene 5' and 3'	K562	blood
14	chr5:40831800-40833600	Genic enhancers	Stomach Mucosa	stomach
15	chr5:40831800-40834800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
16	chr5:40831800-40835000	Transcr. at gene 5' and 3'	A549	lung
17	chr5:40831800-40835200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
18	chr5:40832000-40833800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:40832000-40835000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
20	chr5:40832000-40835200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
21	chr5:40832200-40833600	Genic enhancers	Liver	Liver
22	chr5:40832200-40833800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:40832200-40834600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
26	chr5:40832200-40834600	Transcr. at gene 5' and 3'	NH-A	brain
27	chr5:40832200-40835000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
28	chr5:40832200-40835000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
29	chr5:40832400-40834000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr5:40832400-40834800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
31	chr5:40832600-40834000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:40832600-40834000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr5:40832600-40834400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:40832600-40834400	Transcr. at gene 5' and 3'	HepG2	liver
35	chr5:40832600-40834400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
36	chr5:40832600-40834600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr5:40832600-40834600	Transcr. at gene 5' and 3'	HMEC	breast
38	chr5:40832600-40834800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
39	chr5:40832600-40834800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
40	chr5:40832600-40834800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:40832600-40835200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
42	chr5:40832800-40833600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:40832800-40833800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:40832800-40833800	Genic enhancers	Fetal Lung	lung
45	chr5:40832800-40834000	Genic enhancers	Primary B cells from cord blood	blood
46	chr5:40832800-40834000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr5:40832800-40834600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:40832800-40834600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:40832800-40834800	Transcr. at gene 5' and 3'	Osteobl	bone
50	chr5:40832800-40835000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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