Variant report

Variant	rs7253652
Chromosome Location	chr19:45681134-45681135
allele	C/G
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	TBP	chr19:45681058-45682273	Hela-S3	cervix:	n/a	n/a
3	YY1	chr19:45681052-45683147	GM12878	blood:	n/a	n/a
4	FOS	chr19:45680982-45682029	MCF10A-Er-Src	breast:	n/a	chr19:45681985-45681994 chr19:45681607-45681616 chr19:45681807-45681821 chr19:45681520-45681529
5	REST	chr19:45680904-45682692	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr19:45681047-45682441	U87	brain:	n/a	n/a
7	POLR2A	chr19:45680971-45682274	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr19:45681009-45682042	A549	lung:	n/a	n/a
9	YY1	chr19:45681080-45681729	K562	blood:	n/a	n/a
10	YY1	chr19:45681076-45681816	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFIC	chr19:45681080-45682202	HepG2	liver:	n/a	n/a
12	MXI1	chr19:45681014-45683063	GM12878	blood:	n/a	chr19:45681954-45681963
13	BHLHE40	chr19:45680931-45683148	K562	blood:	n/a	chr19:45682072-45682088
14	CREB1	chr19:45680899-45682442	K562	blood:	n/a	n/a
15	SIN3AK20	chr19:45680879-45682979	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:45681125-45682363	H1-neurons	neurons:	n/a	n/a
17	MAX	chr19:45681088-45682737	SK-N-SH	brain:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
18	CREB1	chr19:45681002-45683025	GM12878	blood:	n/a	n/a
19	ELF1	chr19:45680935-45682821	HCT-116	colon:	n/a	chr19:45682207-45682218 chr19:45681727-45681738 chr19:45681728-45681737 chr19:45681726-45681739 chr19:45682208-45682217 chr19:45681727-45681738
20	TAF1	chr19:45680923-45681736	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr19:45680986-45682870	A549	lung:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
22	FOS	chr19:45680960-45682102	MCF10A-Er-Src	breast:	n/a	chr19:45681985-45681994 chr19:45681607-45681616 chr19:45681807-45681821 chr19:45681520-45681529
23	STAT3	chr19:45681031-45681188	MCF10A-Er-Src	breast:	n/a	n/a
24	TAF1	chr19:45681100-45681777	HepG2	liver:	n/a	n/a
25	POLR2A	chr19:45681079-45682506	Raji	blood:	n/a	n/a
26	FOSL2	chr19:45680903-45682540	A549	lung:	n/a	chr19:45681985-45681994 chr19:45681607-45681616 chr19:45681807-45681821 chr19:45681520-45681529
27	MAX	chr19:45680927-45682588	A549	lung:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
28	POLR2A	chr19:45681099-45682657	HCT-116	colon:	n/a	n/a
29	POLR2A	chr19:45681126-45681594	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr19:45680901-45682654	ECC-1	luminal epithelium:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
31	MAZ	chr19:45681016-45683307	K562	blood:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
32	ELF1	chr19:45680991-45683266	GM12878	blood:	n/a	chr19:45682207-45682218 chr19:45681727-45681738 chr19:45681728-45681737 chr19:45681726-45681739 chr19:45682208-45682217 chr19:45681727-45681738
33	SRF	chr19:45680939-45682348	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:45680897-45681681	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr19:45681134-45682953	GM10847	blood:	n/a	n/a
36	MYC	chr19:45680936-45682447	MCF10A-Er-Src	breast:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
37	CEBPB	chr19:45681025-45682247	Hela-S3	cervix:	n/a	n/a
38	GTF2F1	chr19:45681079-45682275	Hela-S3	cervix:	n/a	n/a
39	TBP	chr19:45681130-45682487	K562	blood:	n/a	n/a
40	MAX	chr19:45681087-45683103	GM12878	blood:	n/a	chr19:45681477-45681487 chr19:45681628-45681644 chr19:45681956-45681964
41	TAF1	chr19:45681059-45681623	A549	lung:	n/a	n/a
42	ATF1	chr19:45681004-45682199	K562	blood:	n/a	n/a
43	JUND	chr19:45681081-45682273	K562	blood:	n/a	chr19:45681985-45681994 chr19:45681607-45681616 chr19:45681807-45681821 chr19:45681520-45681529
44	ELF1	chr19:45681053-45682489	K562	blood:	n/a	chr19:45682207-45682218 chr19:45681727-45681738 chr19:45681728-45681737 chr19:45681726-45681739 chr19:45682208-45682217 chr19:45681727-45681738
45	SRF	chr19:45681082-45682168	ECC-1	luminal epithelium:	n/a	n/a
46	SIN3AK20	chr19:45680931-45682519	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr19:45680973-45683051	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr19:45681126-45681674	GM15510	blood:	n/a	n/a
49	RCOR1	chr19:45681125-45682479	Hela-S3	cervix:	n/a	n/a
50	SIX5	chr19:45680688-45682503	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45680180..45683713-chr19:45733323..45737109,3	K562	blood:
2	chr19:45658848..45663469-chr19:45680259..45684163,6	MCF-7	breast:
3	chr19:45578352..45580821-chr19:45679388..45681588,2	K562	blood:
4	chr19:45654421..45658397-chr19:45679888..45682724,3	K562	blood:
5	chr19:45644450..45646816-chr19:45679774..45683109,3	MCF-7	breast:
6	chr19:45679504..45683518-chr19:45685241..45688488,5	MCF-7	breast:
7	chr19:45503982..45506844-chr19:45681115..45683310,3	K562	blood:
8	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:
9	chr19:45680559..45684359-chr19:45688843..45692525,5	MCF-7	breast:
10	chr19:45655086..45657605-chr19:45680853..45682730,2	MCF-7	breast:

Variant related genes	Relation type
BLOC1S3	TF binding region
ENSG00000267545	TF binding region
ENSG00000104856	Chromatin interaction
ENSG00000266958	Chromatin interaction
ENSG00000130201	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000225157	Chromatin interaction
ENSG00000179846	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10405306	0.81[CEU][hapmap]
rs10409138	0.84[CEU][hapmap]
rs10421932	0.84[CEU][hapmap]
rs11881409	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs12460041	1.00[GIH][hapmap]
rs17562676	1.00[MKK][hapmap]
rs6509200	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7248168	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73564239	0.95[EUR][1000 genomes]
rs73564247	0.95[EUR][1000 genomes]
rs8104024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8106106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
9	esv1791796	chr19:45673701-45681988	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7253652	Hs.466924	cis	multi-tissue	Pritchard
rs7253652	VN1R2	cis	parietal	SCAN
rs7253652	AP2A1	cis	cerebellum	SCAN
rs7253652	NANOS2	cis	cerebellum	SCAN
rs7253652	CCDC8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45680200-45681400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr19:45680200-45683200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:45680200-45684400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:45680400-45681200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr19:45680400-45681200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:45680400-45681200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:45680400-45681200	Flanking Active TSS	Dnd41	blood
8	chr19:45680400-45681400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:45680400-45681400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr19:45680400-45682200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:45680400-45682800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:45680400-45683200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:45680400-45683200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:45680400-45683200	Active TSS	GM12878-XiMat	blood
15	chr19:45680400-45683200	Active TSS	Hela-S3	cervix
16	chr19:45680400-45683400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:45680400-45683600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:45680400-45683600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:45680400-45683600	Active TSS	K562	blood
20	chr19:45680400-45683800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:45680600-45681200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr19:45680600-45681200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:45680600-45681200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:45680600-45681200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:45680600-45681200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:45680600-45681200	Flanking Active TSS	Liver	Liver
27	chr19:45680600-45681200	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr19:45680600-45681200	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr19:45680600-45681200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr19:45680600-45681200	Flanking Active TSS	Fetal Brain Female	brain
31	chr19:45680600-45681600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr19:45680600-45683000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:45680600-45683000	Active TSS	Osteobl	bone
34	chr19:45680600-45683200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:45680600-45683200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:45680600-45683200	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr19:45680600-45683200	Active TSS	Fetal Intestine Large	intestine
38	chr19:45680600-45683400	Active TSS	H1 Cell Line	embryonic stem cell
39	chr19:45680600-45683400	Active TSS	Rectal Smooth Muscle	rectum
40	chr19:45680600-45683600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:45680600-45683600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr19:45680600-45683600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:45680800-45681200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr19:45680800-45681200	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr19:45680800-45681200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:45680800-45681200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr19:45680800-45681200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:45680800-45681200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr19:45680800-45681200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:45680800-45681200	Flanking Active TSS	Brain Angular Gyrus	brain

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