Variant report

Variant	rs6509200
Chromosome Location	chr19:45683448-45683449
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45681036-45683898	K562	blood:	n/a	n/a
2	MTA3	chr19:45683002-45683466	GM12878	blood:	n/a	n/a
3	UBTF	chr19:45681902-45683452	K562	blood:	n/a	n/a
4	POLR2A	chr19:45680959-45683780	K562	blood:	n/a	n/a
5	ZNF384	chr19:45683298-45683683	K562	blood:	n/a	n/a
6	MXI1	chr19:45680750-45683498	IMR90	lung:	n/a	chr19:45681954-45681963
7	RFX5	chr19:45680747-45683462	IMR90	lung:	n/a	chr19:45681521-45681530
8	UBTF	chr19:45681963-45683597	K562	blood:	n/a	n/a
9	MAZ	chr19:45680655-45683458	IMR90	lung:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
10	CHD1	chr19:45680380-45683531	IMR90	lung:	n/a	chr19:45681612-45681622
11	MXI1	chr19:45680836-45683576	SK-N-SH	brain:	n/a	chr19:45681954-45681963
12	MYC	chr19:45680674-45683543	A549	lung:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964

No.	Distal block	Cell Line	Cell type
1	chr19:45594755..45598539-chr19:45681810..45685400,4	K562	blood:
2	chr19:45594586..45596499-chr19:45682181..45685187,4	MCF-7	breast:
3	chr19:45680180..45683713-chr19:45733323..45737109,3	K562	blood:
4	chr19:45658848..45663469-chr19:45680259..45684163,6	MCF-7	breast:
5	chr19:45581068..45583958-chr19:45681428..45684016,2	K562	blood:
6	chr19:45639686..45641880-chr19:45681901..45684356,2	MCF-7	breast:
7	chr19:45679504..45683518-chr19:45685241..45688488,5	MCF-7	breast:
8	chr19:45681420..45684587-chr19:45687242..45692393,7	MCF-7	breast:
9	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:
10	chr19:45541123..45542652-chr19:45681977..45683668,2	MCF-7	breast:
11	chr19:45681162..45683480-chr19:45842144..45844672,3	K562	blood:
12	chr19:45680559..45684359-chr19:45688843..45692525,5	MCF-7	breast:
13	chr19:45652567..45654233-chr19:45681921..45683559,2	MCF-7	breast:
14	chr19:45594874..45597676-chr19:45681810..45683655,2	K562	blood:

Variant related genes	Relation type
TRAPPC6A	TF binding region
ENSG00000104859	Chromatin interaction
ENSG00000130201	Chromatin interaction
ENSG00000179846	Chromatin interaction
ENSG00000266958	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000225157	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000267044	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000104892	Chromatin interaction
ENSG00000268341	Chromatin interaction
ENSG00000267037	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10405306	0.81[CEU][hapmap]
rs10409138	0.84[CEU][hapmap]
rs10421932	0.84[CEU][hapmap]
rs1048552	0.85[AFR][1000 genomes]
rs11881409	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs12459817	0.88[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12460041	1.00[GIH][hapmap]
rs12460178	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12461733	0.88[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12463327	0.85[AFR][1000 genomes]
rs56796781	0.91[AFR][1000 genomes]
rs57302271	0.85[AFR][1000 genomes]
rs57627123	0.85[AFR][1000 genomes]
rs58504789	0.85[AFR][1000 genomes]
rs59215448	0.85[AFR][1000 genomes]
rs7248168	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7253652	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73564216	0.85[AFR][1000 genomes]
rs73564219	0.85[AFR][1000 genomes]
rs73564221	0.85[AFR][1000 genomes]
rs73564225	0.85[AFR][1000 genomes]
rs73564232	0.85[AFR][1000 genomes]
rs73564235	0.85[AFR][1000 genomes]
rs73564239	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73564240	0.85[AFR][1000 genomes]
rs73564245	0.85[AFR][1000 genomes]
rs73564247	0.95[EUR][1000 genomes]
rs73564250	0.85[AFR][1000 genomes]
rs73564265	0.85[AFR][1000 genomes]
rs8104024	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8106106	0.99[EUR][1000 genomes]
rs8110379	1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1794498	chr19:45673701-45691040	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv1005203	chr19:45675812-45684868	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2422482	chr19:45676705-45769805	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	esv1794901	chr19:45681661-45690775	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv3364426	chr19:45681962-45684010	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6509200	NANOS2	cis	cerebellum	SCAN
rs6509200	AP2A1	cis	cerebellum	SCAN
rs6509200	ZNF285	cis	lymphoblastoid	seeQTL
rs6509200	CCDC8	cis	parietal	SCAN
rs6509200	VN1R2	cis	parietal	SCAN
rs6509200	Hs.466924	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45680200-45684400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:45680400-45683600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:45680400-45683600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:45680400-45683600	Active TSS	K562	blood
5	chr19:45680400-45683800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:45680600-45683600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:45680600-45683600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr19:45680600-45683600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:45680800-45683600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:45681000-45683600	Active TSS	HSMMtube	muscle
11	chr19:45682200-45683600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:45682200-45683600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:45682200-45683600	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr19:45682200-45683800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr19:45682400-45683600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:45682400-45683600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr19:45682400-45683800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr19:45682400-45684000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:45682600-45683600	Enhancers	Fetal Heart	heart
20	chr19:45682600-45683600	Active TSS	HepG2	liver
21	chr19:45682600-45684000	Enhancers	Fetal Brain Male	brain
22	chr19:45682600-45686600	Weak transcription	Fetal Kidney	kidney
23	chr19:45682800-45683600	Flanking Active TSS	Thymus	Thymus
24	chr19:45682800-45683800	Flanking Active TSS	Right Ventricle	heart
25	chr19:45682800-45684000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr19:45682800-45685200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:45683000-45683600	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr19:45683000-45683600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr19:45683000-45683600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:45683000-45683600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:45683000-45683600	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr19:45683000-45683600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr19:45683000-45683600	Flanking Active TSS	Osteobl	bone
34	chr19:45683000-45683800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr19:45683000-45683800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:45683000-45683800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr19:45683000-45683800	Flanking Active TSS	HMEC	breast
38	chr19:45683000-45684000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:45683000-45685000	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr19:45683200-45683600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr19:45683200-45683600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:45683200-45683600	Enhancers	Brain Anterior Caudate	brain
43	chr19:45683200-45683600	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr19:45683200-45683600	Flanking Active TSS	Placenta	Placenta
45	chr19:45683200-45683600	Flanking Active TSS	Psoas Muscle	Psoas
46	chr19:45683200-45683600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
47	chr19:45683200-45683600	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr19:45683200-45683600	Flanking Active TSS	NHLF	lung
49	chr19:45683200-45683800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr19:45683200-45683800	Enhancers	Brain Cingulate Gyrus	brain

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