Variant report

Variant	rs10411704
Chromosome Location	chr19:35800662-35800663
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr19:35800621-35800926	K562	blood:	n/a	n/a
2	MAX	chr19:35800404-35801160	K562	blood:	n/a	chr19:35801098-35801108
3	RXRA	chr19:35800292-35800902	HepG2	liver:	n/a	n/a
4	NR2F2	chr19:35800212-35801394	K562	blood:	n/a	chr19:35801172-35801187
5	CTCF	chr19:35800640-35800790	HepG2	liver:	n/a	n/a
6	TBL1XR1	chr19:35800353-35801089	K562	blood:	n/a	n/a
7	RCOR1	chr19:35799869-35801133	K562	blood:	n/a	n/a
8	HMGN3	chr19:35800559-35801136	K562	blood:	n/a	n/a
9	E2F6	chr19:35800380-35801086	K562	blood:	n/a	n/a
10	EGR1	chr19:35800357-35801153	K562	blood:	n/a	n/a
11	CEBPB	chr19:35800410-35800834	K562	blood:	n/a	n/a
12	MAX	chr19:35800313-35801402	K562	blood:	n/a	chr19:35801098-35801108
13	UBTF	chr19:35800441-35801055	K562	blood:	n/a	n/a
14	EP300	chr19:35800364-35800683	K562	blood:	n/a	n/a
15	HEY1	chr19:35800474-35801112	K562	blood:	n/a	n/a
16	POLR2A	chr19:35799932-35801269	K562	blood:	n/a	n/a
17	TBP	chr19:35800413-35801217	K562	blood:	n/a	n/a
18	ESR1	chr19:35800368-35800720	T-47D	breast:	n/a	n/a
19	JUND	chr19:35800242-35801139	K562	blood:	n/a	n/a
20	RXRA	chr19:35800237-35800777	HepG2	liver:	n/a	n/a
21	EP300	chr19:35800267-35800725	HepG2	liver:	n/a	n/a
22	RCOR1	chr19:35800544-35801078	K562	blood:	n/a	n/a
23	FOXA1	chr19:35800256-35800700	HepG2	liver:	n/a	n/a
24	NR2F2	chr19:35800201-35801218	K562	blood:	n/a	chr19:35801172-35801187
25	MAX	chr19:35800401-35801168	K562	blood:	n/a	chr19:35801098-35801108
26	MYC	chr19:35800407-35801176	K562	blood:	n/a	chr19:35801098-35801108
27	BHLHE40	chr19:35800541-35801165	K562	blood:	n/a	n/a
28	POLR2A	chr19:35800620-35800784	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:35800385-35800960	K562	blood:	n/a	n/a
30	TEAD4	chr19:35800084-35801153	K562	blood:	n/a	n/a
31	TEAD4	chr19:35800130-35800723	HepG2	liver:	n/a	n/a
32	KAP1	chr19:35800361-35800662	U2OS	brain:	n/a	n/a
33	ESR1	chr19:35800423-35800687	T-47D	breast:	n/a	n/a
34	FOXA1	chr19:35800344-35800711	HepG2	liver:	n/a	n/a
35	FOXA2	chr19:35800340-35800708	HepG2	liver:	n/a	n/a
36	CEBPB	chr19:35800318-35800664	K562	blood:	n/a	n/a
37	YY1	chr19:35800383-35801230	K562	blood:	n/a	n/a
38	HA-E2F1	chr19:35800252-35800789	MCF-7	breast:	n/a	n/a
39	GATA3	chr19:35800345-35800849	MCF-7	breast:	n/a	n/a
40	ESR1	chr19:35800415-35800722	T-47D	breast:	n/a	n/a
41	E2F6	chr19:35800379-35801676	K562	blood:	n/a	n/a
42	MYC	chr19:35800369-35801180	K562	blood:	n/a	chr19:35801098-35801108
43	TEAD4	chr19:35800338-35800753	K562	blood:	n/a	n/a
44	POLR2A	chr19:35800332-35800720	K562	blood:	n/a	n/a
45	EP300	chr19:35800406-35800734	HepG2	liver:	n/a	n/a
46	HDAC2	chr19:35800365-35800694	HepG2	liver:	n/a	n/a
47	YY1	chr19:35800482-35800706	K562	blood:	n/a	n/a
48	MYBL2	chr19:35800295-35800720	HepG2	liver:	n/a	n/a
49	ZBTB7A	chr19:35800435-35801025	K562	blood:	n/a	n/a
50	TAF1	chr19:35800410-35800881	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:35738491..35740445-chr19:35800431..35803185,3	MCF-7	breast:
2	chr19:35757352..35763490-chr19:35798817..35804347,10	MCF-7	breast:
3	chr19:35781735..35783754-chr19:35799663..35801226,2	MCF-7	breast:
4	chr19:35738675..35740393-chr19:35799543..35801412,2	MCF-7	breast:
5	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:
6	chr19:35800092..35801659-chr19:35829023..35831587,2	K562	blood:

No data

Variant related genes	Relation type
MAG	TF binding region
ENSG00000105695	Chromatin interaction
ENSG00000012124	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000105699	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10411883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11669734	1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2301151	0.82[ASW][hapmap]
rs6510480	0.91[AFR][1000 genomes]
rs7251526	0.88[MEX][hapmap];1.00[MKK][hapmap]
rs756796	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv9711	chr19:35797190-35805196	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
10	esv1006379	chr19:35798572-35810821	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10411704	MIR5196	cis	Thyroid	GTEx
rs10411704	MAG	cis	Artery Aorta	GTEx
rs10411704	U62631.5	cis	Thyroid	GTEx
rs10411704	RPS16	cis	parietal	SCAN
rs10411704	FFAR1	cis	lung	GTEx
rs10411704	ADCK4	cis	cerebellum	SCAN
rs10411704	MAG	cis	Thyroid	GTEx
rs10411704	MAG	cis	Esophagus Muscularis	GTEx
rs10411704	FFAR1	cis	Thyroid	GTEx
rs10411704	CD22	cis	lung	GTEx
rs10411704	MAG	cis	Stomach	GTEx
rs10411704	MAG	cis	lung	GTEx
rs10411704	CD22	cis	Thyroid	GTEx
rs10411704	MAG	cis	multi-tissue	Pritchard
rs10411704	CD22	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35774800-35809600	Weak transcription	Right Atrium	heart
2	chr19:35792800-35801400	Genic enhancers	Brain Hippocampus Middle	brain
3	chr19:35794400-35810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:35796800-35801000	Weak transcription	Fetal Thymus	thymus
5	chr19:35797000-35800800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:35797200-35802200	Weak transcription	Brain Anterior Caudate	brain
7	chr19:35797600-35804000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:35797800-35800800	Genic enhancers	Brain Substantia Nigra	brain
9	chr19:35797800-35809600	Weak transcription	Brain Angular Gyrus	brain
10	chr19:35798000-35801400	Enhancers	Fetal Muscle Trunk	muscle
11	chr19:35798000-35801800	Enhancers	Fetal Stomach	stomach
12	chr19:35798000-35802600	Enhancers	Placenta	Placenta
13	chr19:35798200-35801400	Enhancers	Fetal Muscle Leg	muscle
14	chr19:35798200-35802800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:35798200-35811400	Weak transcription	Liver	Liver
16	chr19:35799200-35801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:35799200-35804000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:35799400-35800800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:35799400-35804200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:35799600-35801400	Genic enhancers	Brain Cingulate Gyrus	brain
21	chr19:35799600-35803400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr19:35799800-35801200	Enhancers	Duodenum Mucosa	Duodenum
23	chr19:35800000-35801000	Enhancers	Lung	lung
24	chr19:35800000-35801000	Enhancers	Hela-S3	cervix
25	chr19:35800000-35801600	Flanking Active TSS	K562	blood
26	chr19:35800000-35801800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:35800000-35801800	Flanking Active TSS	Fetal Lung	lung
28	chr19:35800000-35803800	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr19:35800000-35804000	Weak transcription	Primary B cells from cord blood	blood
30	chr19:35800200-35800800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:35800200-35801000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr19:35800200-35801000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr19:35800200-35801000	Enhancers	Fetal Intestine Small	intestine
34	chr19:35800200-35801200	Enhancers	Fetal Intestine Large	intestine
35	chr19:35800200-35801400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:35800200-35801400	Enhancers	Pancreas	Pancrea
37	chr19:35800200-35803400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr19:35800400-35800800	Enhancers	Right Ventricle	heart
39	chr19:35800400-35800800	Enhancers	GM12878-XiMat	blood
40	chr19:35800400-35800800	Flanking Active TSS	HepG2	liver
41	chr19:35800400-35801000	Enhancers	Fetal Heart	heart
42	chr19:35800400-35802600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:35800600-35800800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr19:35800600-35801200	Active TSS	Fetal Kidney	kidney
45	chr19:35800600-35801600	Enhancers	Spleen	Spleen
46	chr19:35800600-35802000	Enhancers	HMEC	breast
47	chr19:35800600-35803400	Flanking Active TSS	Ovary	ovary

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