Variant report

Variant	rs10404602
Chromosome Location	chr19:37825633-37825634
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:207)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:207 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr19:37825193-37825880	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr19:37825306-37825716	GM12878	blood:	n/a	n/a
3	NFYB	chr19:37825426-37825640	GM12878	blood:	n/a	n/a
4	EBF1	chr19:37825293-37825675	GM12878	blood:	n/a	chr19:37825478-37825489
5	SP1	chr19:37825172-37825723	GM12878	blood:	n/a	n/a
6	GABPA	chr19:37825287-37825682	GM12878	blood:	n/a	n/a
7	CTCF	chr19:37825520-37825670	BJ	skin:	n/a	n/a
8	KAP1	chr19:37825208-37825809	HEK293	kidney:	n/a	n/a
9	ELF1	chr19:37824960-37825923	MCF-7	breast:	n/a	n/a
10	POLR2A	chr19:37824917-37826052	H1-hESC	embryonic stem cell:	n/a	n/a
11	CREB1	chr19:37825063-37825856	H1-hESC	embryonic stem cell:	n/a	n/a
12	PAX5	chr19:37825173-37825784	GM12878	blood:	n/a	chr19:37825550-37825559 chr19:37825500-37825509
13	POLR2A	chr19:37825413-37825837	GM18505	blood:	n/a	n/a
14	POLR2A	chr19:37825280-37825806	GM12891	blood:	n/a	n/a
15	POLR2A	chr19:37825471-37825790	Gliobla	brain:	n/a	n/a
16	POLR2A	chr19:37825101-37826044	PFSK-1	brain:	n/a	n/a
17	RCOR1	chr19:37825393-37825800	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr19:37825476-37825662	MCF10A-Er-Src	breast:	n/a	chr19:37825510-37825522
19	POLR2A	chr19:37825408-37825785	MCF10A-Er-Src	breast:	n/a	n/a
20	TAF1	chr19:37825313-37825738	PFSK-1	brain:	n/a	n/a
21	SPI1	chr19:37825269-37825744	HL-60	blood:	n/a	n/a
22	FOXA1	chr19:37825394-37825690	T-47D	breast:	n/a	n/a
23	CTCF	chr19:37825520-37825670	HCPEpiC	choroid plexus:	n/a	n/a
24	POLR2A	chr19:37825231-37825906	GM12878	blood:	n/a	n/a
25	ATF2	chr19:37825260-37825798	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:37824986-37826276	GM12878	blood:	n/a	n/a
27	WRNIP1	chr19:37825355-37825812	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:37825004-37826021	MCF-7	breast:	n/a	n/a
29	YY1	chr19:37825356-37825688	SK-N-SH_RA	brain:	n/a	n/a
30	TAF1	chr19:37825396-37825674	GM12878	blood:	n/a	n/a
31	MYC	chr19:37825578-37825670	HUVEC	blood vessel:	n/a	n/a
32	MAZ	chr19:37825133-37825781	Hela-S3	cervix:	n/a	n/a
33	POU2F2	chr19:37825496-37825684	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:37825515-37825667	K562	blood:	n/a	n/a
35	RFX5	chr19:37825281-37825756	GM12878	blood:	n/a	chr19:37825332-37825341
36	POLR2A	chr19:37825168-37826075	GM12891	blood:	n/a	n/a
37	SPI1	chr19:37825324-37825664	GM12878	blood:	n/a	n/a
38	CEBPB	chr19:37825384-37825743	Hela-S3	cervix:	n/a	n/a
39	TBP	chr19:37825064-37825865	H1-hESC	embryonic stem cell:	n/a	n/a
40	TBP	chr19:37825385-37825725	Hela-S3	cervix:	n/a	n/a
41	MYC	chr19:37825513-37825711	MCF-7	breast:	n/a	n/a
42	POLR2A	chr19:37825295-37825984	GM12892	blood:	n/a	n/a
43	POLR2A	chr19:37824898-37825984	H1-hESC	embryonic stem cell:	n/a	n/a
44	MXI1	chr19:37824749-37826961	SK-N-SH	brain:	n/a	n/a
45	MXI1	chr19:37825388-37825860	Hela-S3	cervix:	n/a	n/a
46	STAT1	chr19:37825294-37825777	GM12878	blood:	n/a	chr19:37825510-37825522
47	POLR2A	chr19:37825005-37825946	MCF-7	breast:	n/a	n/a
48	POLR2A	chr19:37825369-37825793	Hela-S3	cervix:	n/a	n/a
49	GABPA	chr19:37825412-37825665	K562	blood:	n/a	n/a
50	POLR2A	chr19:37824978-37826034	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:37740273..37743128-chr19:37823150..37825762,2	MCF-7	breast:
2	chr19:37824652..37827295-chr19:37827971..37830773,4	MCF-7	breast:
3	chr19:37822549..37827431-chr19:37836072..37838954,4	MCF-7	breast:
4	chr19:37807599..37810002-chr19:37824275..37826787,2	MCF-7	breast:
5	chr19:37806982..37809957-chr19:37825534..37828988,3	MCF-7	breast:
6	chr19:37825178..37827025-chr19:37995882..37998065,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF527-1	chr19:37825573-37825684	NONHSAT066104

No data

Variant related genes	Relation type
ENSG00000267682	TF binding region
ENSG00000266916	Chromatin interaction
ENSG00000226686	Chromatin interaction
ENSG00000188227	Chromatin interaction
ENSG00000181666	Chromatin interaction
ENSG00000267682	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1015848	0.84[EUR][1000 genomes]
rs1015849	0.84[EUR][1000 genomes]
rs1035479	0.84[EUR][1000 genomes]
rs10403582	0.82[EUR][1000 genomes]
rs10403613	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404920	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10405064	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10405325	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10405407	0.96[EUR][1000 genomes]
rs10406177	0.82[EUR][1000 genomes]
rs10407084	0.84[EUR][1000 genomes]
rs10409204	0.86[EUR][1000 genomes]
rs10412043	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10413602	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10414904	0.96[EUR][1000 genomes]
rs10415024	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415937	0.96[EUR][1000 genomes]
rs10417503	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10417844	0.96[EUR][1000 genomes]
rs10420430	0.87[EUR][1000 genomes]
rs10422074	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10422423	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10422667	0.84[EUR][1000 genomes]
rs10422967	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424574	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10426297	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426618	0.84[EUR][1000 genomes]
rs10426666	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426699	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12104380	0.95[EUR][1000 genomes]
rs12104381	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709812	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12709813	0.96[EUR][1000 genomes]
rs12972252	0.84[EUR][1000 genomes]
rs12979470	0.83[EUR][1000 genomes]
rs12981532	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12982333	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13343471	0.86[EUR][1000 genomes]
rs13343485	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13343502	0.82[EUR][1000 genomes]
rs13345116	0.96[EUR][1000 genomes]
rs13345148	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1373991	0.96[EUR][1000 genomes]
rs1559229	0.89[EUR][1000 genomes]
rs1823061	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112923	0.82[EUR][1000 genomes]
rs2303131	0.86[EUR][1000 genomes]
rs28402338	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28538699	0.82[EUR][1000 genomes]
rs28623164	0.83[EUR][1000 genomes]
rs2891699	0.83[EUR][1000 genomes]
rs34544865	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34603719	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35085437	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35777021	0.86[EUR][1000 genomes]
rs3745765	0.94[EUR][1000 genomes]
rs3760825	0.82[EUR][1000 genomes]
rs3803895	0.84[EUR][1000 genomes]
rs4417644	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4452075	0.90[EUR][1000 genomes]
rs4801759	0.84[EUR][1000 genomes]
rs4801803	0.82[EUR][1000 genomes]
rs4802766	0.80[EUR][1000 genomes]
rs4803229	0.92[EUR][1000 genomes]
rs4803347	0.96[EUR][1000 genomes]
rs4803460	0.84[EUR][1000 genomes]
rs4803539	0.84[EUR][1000 genomes]
rs4969487	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57795776	0.85[EUR][1000 genomes]
rs6508711	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508713	0.89[EUR][1000 genomes]
rs6508714	0.89[EUR][1000 genomes]
rs6508715	0.89[EUR][1000 genomes]
rs6508716	0.97[EUR][1000 genomes]
rs6508719	0.89[EUR][1000 genomes]
rs67293224	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713256	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7246993	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7247259	0.96[EUR][1000 genomes]
rs7252099	0.86[EUR][1000 genomes]
rs7252325	0.83[EUR][1000 genomes]
rs7252346	0.83[EUR][1000 genomes]
rs7255407	0.83[EUR][1000 genomes]
rs7255972	0.86[EUR][1000 genomes]
rs7256130	0.80[EUR][1000 genomes]
rs7257495	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7257672	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7258692	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259968	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7408133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7408446	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7408563	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109632	0.83[EUR][1000 genomes]
rs8111782	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8112610	0.80[EUR][1000 genomes]
rs9304566	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9676967	0.83[EUR][1000 genomes]
rs9917081	0.92[EUR][1000 genomes];0.81[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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37823400-37827200	ZNF genes & repeats	A549	lung
2	chr19:37824200-37826200	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr19:37824400-37826400	Active TSS	Colonic Mucosa	Colon
4	chr19:37824600-37826800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
5	chr19:37824800-37825800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:37824800-37826000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
7	chr19:37824800-37826000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:37824800-37826000	Active TSS	Fetal Brain Female	brain
9	chr19:37824800-37826000	ZNF genes & repeats	Lung	lung
10	chr19:37824800-37826000	Active TSS	Small Intestine	intestine
11	chr19:37824800-37826200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:37824800-37826200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr19:37824800-37826200	Active TSS	Fetal Intestine Large	intestine
14	chr19:37824800-37826200	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:37824800-37826200	Active TSS	Right Atrium	heart
16	chr19:37824800-37826400	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr19:37824800-37826400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:37824800-37826600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr19:37824800-37826600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:37825000-37825800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr19:37825000-37826000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr19:37825000-37826000	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr19:37825000-37826000	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr19:37825000-37826000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:37825000-37826000	Active TSS	Hela-S3	cervix
26	chr19:37825000-37826200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:37825000-37826200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr19:37825000-37826200	Active TSS	Placenta Amnion	Placenta Amnion
29	chr19:37825000-37826400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:37825000-37826400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:37825000-37826400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:37825000-37826400	Active TSS	Aorta	Aorta
33	chr19:37825000-37826400	Flanking Active TSS	Placenta	Placenta
34	chr19:37825000-37826600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr19:37825000-37826600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr19:37825000-37826800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:37825000-37826800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:37825200-37825800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:37825200-37825800	Active TSS	Brain Cingulate Gyrus	brain
40	chr19:37825200-37825800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:37825200-37825800	Active TSS	Fetal Heart	heart
42	chr19:37825200-37825800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
43	chr19:37825200-37826000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:37825200-37826000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:37825200-37826000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:37825200-37826000	Active TSS	Brain Angular Gyrus	brain
47	chr19:37825200-37826000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr19:37825200-37826000	Active TSS	Brain Substantia Nigra	brain
49	chr19:37825200-37826000	Active TSS	Colon Smooth Muscle	Colon
50	chr19:37825200-37826000	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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