Variant report

Variant	rs10065570
Chromosome Location	chr5:40835627-40835628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:518)
CpG islands
(count:0)
Chromatin interactive
region (count:75)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:518 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40833886-40836321	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:40824786-40836349	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:40833397-40836297	GM15510	blood:	n/a	n/a
4	MAZ	chr5:40834190-40836857	K562	blood:	n/a	n/a
5	RCOR1	chr5:40834861-40836655	K562	blood:	n/a	n/a
6	POLR2A	chr5:40833540-40836475	HL-60	blood:	n/a	n/a
7	ZNF143	chr5:40834899-40835769	K562	blood:	n/a	n/a
8	POLR2A	chr5:40834908-40836491	ProgFib	skin:	n/a	n/a
9	GTF2F1	chr5:40834330-40836510	Hela-S3	cervix:	n/a	n/a
10	TAF1	chr5:40834886-40835816	GM12891	blood:	n/a	n/a
11	TBL1XR1	chr5:40834825-40835856	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
13	TEAD4	chr5:40835042-40835913	ECC-1	luminal epithelium:	n/a	n/a
14	TAF1	chr5:40834831-40835817	GM12878	blood:	n/a	n/a
15	YY1	chr5:40835111-40835941	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZBTB7A	chr5:40835029-40835654	K562	blood:	n/a	n/a
17	RAD21	chr5:40835195-40835884	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYC	chr5:40833754-40836963	K562	blood:	n/a	n/a
19	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
20	REST	chr5:40835128-40835739	SK-N-SH	brain:	n/a	chr5:40835379-40835392 chr5:40835696-40835709
21	USF1	chr5:40835126-40835634	K562	blood:	n/a	n/a
22	POLR2A	chr5:40835006-40835663	HepG2	liver:	n/a	n/a
23	GABPA	chr5:40835066-40835779	Hela-S3	cervix:	n/a	n/a
24	BCLAF1	chr5:40834871-40835747	K562	blood:	n/a	chr5:40835371-40835380 chr5:40835329-40835338
25	TCF12	chr5:40834868-40835785	ECC-1	luminal epithelium:	n/a	n/a
26	TCF3	chr5:40835043-40835645	GM12878	blood:	n/a	n/a
27	ZNF384	chr5:40835228-40835639	GM12878	blood:	n/a	n/a
28	MAX	chr5:40834464-40836104	GM12878	blood:	n/a	n/a
29	RELA	chr5:40834498-40835751	GM19099	blood:	n/a	n/a
30	MAX	chr5:40834759-40836098	HCT-116	colon:	n/a	n/a
31	TAF1	chr5:40834808-40835973	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD2	chr5:40834004-40836006	K562	blood:	n/a	n/a
33	SETDB1	chr5:40835235-40835725	U2OS	brain:	n/a	n/a
34	YY1	chr5:40834992-40835706	GM12892	blood:	n/a	n/a
35	STAT5A	chr5:40834856-40835691	GM12878	blood:	n/a	n/a
36	E2F6	chr5:40835169-40835800	K562	blood:	n/a	n/a
37	POU2F2	chr5:40834919-40835755	GM12891	blood:	n/a	n/a
38	POLR2A	chr5:40833813-40836384	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
40	POLR2A	chr5:40834909-40835853	MCF-7	breast:	n/a	n/a
41	YY1	chr5:40834933-40835760	HepG2	liver:	n/a	n/a
42	ELF1	chr5:40834740-40835790	GM12878	blood:	n/a	chr5:40835311-40835324 chr5:40835328-40835341
43	ZC3H11A	chr5:40834501-40835759	K562	blood:	n/a	n/a
44	ELF1	chr5:40834782-40835858	MCF-7	breast:	n/a	chr5:40835311-40835324 chr5:40835328-40835341
45	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
46	ETS1	chr5:40834482-40835831	A549	lung:	n/a	chr5:40835326-40835342 chr5:40835368-40835379 chr5:40835363-40835380 chr5:40835366-40835380 chr5:40835369-40835380 chr5:40835329-40835338 chr5:40835327-40835338 chr5:40835370-40835383 chr5:40835327-40835337 chr5:40835363-40835380
47	CREB1	chr5:40835185-40835639	A549	lung:	n/a	n/a
48	GATA3	chr5:40835008-40835781	T-47D	breast:	n/a	n/a
49	ELF1	chr5:40834983-40835719	SK-N-SH	brain:	n/a	chr5:40835311-40835324 chr5:40835328-40835341
50	POLR2A	chr5:40834885-40835908	MCF-7	breast:	n/a	n/a

No data

(count:75 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr1:169074990..169075671-chr5:40835294..40835996,2	Hela-S3	cervix:
2	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
3	chr11:62369006..62369884-chr5:40834874..40835819,3	Hela-S3	cervix:
4	chr15:75660364..75660914-chr5:40834869..40835784,2	Hela-S3	cervix:
5	chr5:40834972..40835658-chr5:108745098..108745778,2	Hela-S3	cervix:
6	chr5:40835597..40836125-chr5:162888436..162888982,2	Hela-S3	cervix:
7	chr5:40755751..40756591-chr5:40835238..40835790,2	K562	blood:
8	chr5:40762484..40765387-chr5:40833487..40838148,4	K562	blood:
9	chr17:56735505..56738016-chr5:40834939..40837272,2	MCF-7	breast:
10	chr10:3827429..3828191-chr5:40835475..40836074,2	Hela-S3	cervix:
11	chr5:40834912..40835984-chr9:140135474..140136132,3	Hela-S3	cervix:
12	chr17:80186846..80187596-chr5:40835173..40835947,2	Hela-S3	cervix:
13	chr3:193853525..193854351-chr5:40834871..40835858,2	Hela-S3	cervix:
14	chr11:118660443..118661695-chr5:40834924..40835628,3	Hela-S3	cervix:
15	chr20:48769811..48770518-chr5:40835118..40835765,2	Hela-S3	cervix:
16	chr1:167906290..167907233-chr5:40835120..40836075,2	Hela-S3	cervix:
17	chr10:1094316..1094876-chr5:40835238..40835957,2	Hela-S3	cervix:
18	chr10:71905933..71906580-chr5:40835047..40835677,2	Hela-S3	cervix:
19	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
20	chr1:165599942..165600511-chr5:40835018..40835753,2	Hela-S3	cervix:
21	chr1:53685765..53686506-chr5:40835625..40836570,2	Hela-S3	cervix:
22	chr3:15643193..15644046-chr5:40835040..40835745,2	Hela-S3	cervix:
23	chr14:102552832..102553654-chr5:40835371..40836347,2	Hela-S3	cervix:
24	chr11:62608645..62609622-chr5:40834990..40836219,4	NB4	blood:
25	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
26	chr1:109618246..109619235-chr5:40834996..40835648,2	Hela-S3	cervix:
27	chr5:40835173..40836258-chr6:2841735..2842376,3	Hela-S3	cervix:
28	chr1:206785233..206785921-chr5:40835050..40835901,2	Hela-S3	cervix:
29	chr14:50086962..50087687-chr5:40835299..40835954,2	Hela-S3	cervix:
30	chr4:140477624..140478159-chr5:40834980..40835944,2	Hela-S3	cervix:
31	chr3:130465224..130465984-chr5:40834852..40835728,2	NB4	blood:
32	chr1:28969517..28970070-chr5:40835274..40835926,2	Hela-S3	cervix:
33	chr5:40833991..40836420-chr5:41902681..41904929,3	K562	blood:
34	chr1:173446175..173446711-chr5:40834996..40835929,2	Hela-S3	cervix:
35	chr5:40834802..40835667-chr6:86388362..86388990,2	Hela-S3	cervix:
36	chr5:40835451..40835981-chrX:139656168..139656669,2	Hela-S3	cervix:
37	chr3:152878782..152879621-chr5:40835099..40835642,2	Hela-S3	cervix:
38	chr11:43380229..43380994-chr5:40835063..40836104,3	Hela-S3	cervix:
39	chr14:105487034..105487793-chr5:40834950..40835755,2	Hela-S3	cervix:
40	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
41	chr11:75110516..75111027-chr5:40835282..40835966,2	Hela-S3	cervix:
42	chr12:98909039..98909709-chr5:40835277..40835917,2	Hela-S3	cervix:
43	chr5:32174003..32174900-chr5:40834879..40836223,4	Hela-S3	cervix:
44	chr20:48806718..48807627-chr5:40834835..40835852,3	Hela-S3	cervix:
45	chr5:40835270..40836182-chr6:99872862..99873800,2	Hela-S3	cervix:
46	chr1:119683147..119683839-chr5:40835486..40836269,2	Hela-S3	cervix:
47	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
48	chr5:40835087..40836243-chr5:179050438..179051510,3	NB4	blood:
49	chr11:118965650..118966489-chr5:40834980..40835878,2	Hela-S3	cervix:
50	chr5:40834913..40835799-chr5:130970493..130971019,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SNORD72	TF binding region
RPL37	TF binding region
ENSG00000114315	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000231365	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000198961	Chromatin interaction
ENSG00000254907	Chromatin interaction
ENSG00000113384	Chromatin interaction
ENSG00000103353	Chromatin interaction
ENSG00000052841	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000196455	Chromatin interaction
ENSG00000170540	Chromatin interaction
ENSG00000169045	Chromatin interaction
ENSG00000141526	Chromatin interaction
ENSG00000188486	Chromatin interaction
ENSG00000158987	Chromatin interaction
ENSG00000116874	Chromatin interaction
ENSG00000229388	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000244687	Chromatin interaction
ENSG00000120656	Chromatin interaction
ENSG00000167785	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000240849	Chromatin interaction
ENSG00000272717	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000168282	Chromatin interaction
ENSG00000143153	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000149273	Chromatin interaction
ENSG00000169592	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000135829	Chromatin interaction
ENSG00000197780	Chromatin interaction
ENSG00000073921	Chromatin interaction
ENSG00000132424	Chromatin interaction
ENSG00000164327	Chromatin interaction
ENSG00000272086	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000067082	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000170948	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000165502	Chromatin interaction
ENSG00000260342	Chromatin interaction
ENSG00000162384	Chromatin interaction
ENSG00000131373	Chromatin interaction
ENSG00000117139	Chromatin interaction
ENSG00000021355	Chromatin interaction
ENSG00000169814	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000145391	Chromatin interaction
ENSG00000143164	Chromatin interaction
ENSG00000120802	Chromatin interaction
ENSG00000143486	Chromatin interaction
ENSG00000244268	Chromatin interaction
ENSG00000110367	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000171161	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000207501	Chromatin interaction
ENSG00000152291	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000259818	Chromatin interaction
ENSG00000101213	Chromatin interaction
ENSG00000170779	Chromatin interaction
ENSG00000080824	Chromatin interaction
ENSG00000105926	Chromatin interaction
ENSG00000124208	Chromatin interaction
ENSG00000103356	Chromatin interaction
ENSG00000149929	Chromatin interaction
ENSG00000156521	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000124529	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1001684	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1002424	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs10041430	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10043245	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10074991	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs1122655	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956019	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956047	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11957736	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13361707	0.87[JPT][hapmap];0.82[YRI][hapmap]
rs1345778	0.81[GIH][hapmap]
rs249440	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs3763074	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805497	0.82[YRI][hapmap]
rs6868517	0.81[GIH][hapmap]
rs6876367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73084490	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7717357	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10065570	NUP155	cis	parietal	SCAN
rs10065570	RPL37	cis	cerebellum	SCAN
rs10065570	FGF10	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40833200-40836400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:40833400-40836000	Active TSS	Right Ventricle	heart
3	chr5:40833400-40836200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:40833600-40836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr5:40833600-40836200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:40833600-40836600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:40833800-40836000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:40833800-40836000	Active TSS	Gastric	stomach
9	chr5:40833800-40836600	Active TSS	Ovary	ovary
10	chr5:40834000-40836400	Active TSS	Colonic Mucosa	Colon
11	chr5:40834000-40836600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr5:40834200-40835800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:40834200-40835800	Active TSS	Sigmoid Colon	Sigmoid Colon
14	chr5:40834200-40835800	Active TSS	Stomach Mucosa	stomach
15	chr5:40834200-40836000	Active TSS	Pancreas	Pancrea
16	chr5:40834200-40836000	Active TSS	Small Intestine	intestine
17	chr5:40834200-40836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:40834200-40836200	Active TSS	Esophagus	oesophagus
19	chr5:40834200-40836200	Active TSS	Fetal Intestine Small	intestine
20	chr5:40834200-40836200	Active TSS	Left Ventricle	heart
21	chr5:40834200-40836400	Active TSS	Placenta Amnion	Placenta Amnion
22	chr5:40834200-40836600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:40834200-40836600	Active TSS	Brain Cingulate Gyrus	brain
24	chr5:40834400-40835800	ZNF genes & repeats	Fetal Brain Male	brain
25	chr5:40834400-40835800	Bivalent/Poised TSS	HepG2	liver
26	chr5:40834400-40836000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:40834400-40836000	Active TSS	Fetal Heart	heart
28	chr5:40834400-40836200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:40834400-40836200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:40834400-40836200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:40834400-40836200	Active TSS	Liver	Liver
32	chr5:40834400-40836200	Active TSS	Fetal Kidney	kidney
33	chr5:40834400-40836400	Active TSS	Aorta	Aorta
34	chr5:40834400-40836400	Active TSS	Lung	lung
35	chr5:40834400-40836400	Active TSS	GM12878-XiMat	blood
36	chr5:40834400-40836400	Active TSS	HSMMtube	muscle
37	chr5:40834400-40836600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:40834400-40836600	Active TSS	Fetal Brain Female	brain
39	chr5:40834400-40836600	Active TSS	Fetal Intestine Large	intestine
40	chr5:40834400-40836600	Active TSS	Psoas Muscle	Psoas
41	chr5:40834600-40835800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr5:40834600-40835800	Active TSS	Fetal Lung	lung
43	chr5:40834600-40835800	Active TSS	Thymus	Thymus
44	chr5:40834600-40835800	Active TSS	Spleen	Spleen
45	chr5:40834600-40836000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:40834600-40836000	Active TSS	Colon Smooth Muscle	Colon
47	chr5:40834600-40836000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr5:40834600-40836000	Active TSS	HMEC	breast
49	chr5:40834600-40836200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr5:40834600-40836200	Active TSS	Rectal Smooth Muscle	rectum

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