Variant report

Variant	rs6511291
Chromosome Location	chr19:21950402-21950403
allele	C/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	CREB1	chr19:21949870-21950621	GM12878	blood:	n/a	n/a
2	CEBPD	chr19:21950215-21950467	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:21949855-21950637	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:21949982-21950586	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:21950105-21950465	Hela-S3	cervix:	n/a	n/a
6	CUX1	chr19:21949945-21950705	K562	blood:	n/a	n/a
7	MAX	chr19:21949865-21950565	K562	blood:	n/a	n/a
8	CEBPB	chr19:21950045-21950640	K562	blood:	n/a	n/a
9	MAZ	chr19:21949927-21950634	HepG2	liver:	n/a	n/a
10	TBP	chr19:21950308-21950550	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr19:21950060-21950512	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:21950087-21950487	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr19:21950091-21950572	SK-N-SH	brain:	n/a	n/a
14	FOS	chr19:21950154-21950637	K562	blood:	n/a	chr19:21950345-21950359
15	GABPA	chr19:21950152-21950685	SK-N-SH	brain:	n/a	n/a
16	MAX	chr19:21950104-21950502	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:21949954-21950639	MCF-7	breast:	n/a	n/a
18	POLR2A	chr19:21949933-21950631	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr19:21949839-21950475	H1-hESC	embryonic stem cell:	n/a	n/a
20	TBP	chr19:21949915-21950585	K562	blood:	n/a	n/a
21	POLR2A	chr19:21949811-21950617	GM12878	blood:	n/a	n/a
22	TAF1	chr19:21950023-21950581	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr19:21949647-21950588	K562	blood:	n/a	n/a
24	BHLHE40	chr19:21949896-21950532	GM12878	blood:	n/a	n/a
25	SIN3A	chr19:21949792-21950536	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:21950111-21950564	HCT-116	colon:	n/a	n/a
27	ARID3A	chr19:21950050-21950688	HepG2	liver:	n/a	n/a
28	CTBP2	chr19:21949936-21950568	H1-hESC	embryonic stem cell:	n/a	n/a
29	HCFC1	chr19:21949905-21950559	K562	blood:	n/a	n/a
30	SP1	chr19:21950208-21950645	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:21950082-21950562	K562	blood:	n/a	n/a
32	MYC	chr19:21949920-21950672	NB4	blood:	n/a	n/a
33	MYC	chr19:21949755-21950590	K562	blood:	n/a	n/a
34	TCF7L2	chr19:21950125-21950501	Hela-S3	cervix:	n/a	n/a
35	RFX5	chr19:21950293-21950564	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr19:21949814-21950560	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:21949719-21950596	MCF10A-Er-Src	breast:	n/a	n/a
38	BHLHE40	chr19:21949802-21950565	K562	blood:	n/a	n/a
39	SP2	chr19:21950210-21950645	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr19:21950195-21950407	SK-N-SH	brain:	n/a	n/a
41	USF2	chr19:21950374-21950552	GM12878	blood:	n/a	n/a
42	HEY1	chr19:21950016-21950616	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:21949869-21950513	K562	blood:	n/a	n/a
44	POLR2A	chr19:21949782-21950592	GM12878	blood:	n/a	n/a
45	GABPA	chr19:21950090-21950681	HL-60	blood:	n/a	n/a
46	JUN	chr19:21950150-21950603	K562	blood:	n/a	chr19:21950345-21950359
47	PML	chr19:21949990-21950571	K562	blood:	n/a	n/a
48	YY1	chr19:21949732-21950441	H1-hESC	embryonic stem cell:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081
49	POLR2A	chr19:21949818-21950611	HL-60	blood:	n/a	n/a
50	YY1	chr19:21949856-21950533	SK-N-SH_RA	brain:	n/a	chr19:21950064-21950075 chr19:21950071-21950093 chr19:21950072-21950080 chr19:21950059-21950073 chr19:21950071-21950081

No.	Distal block	Cell Line	Cell type
1	chr19:21948377..21950622-chr19:22016631..22019164,2	MCF-7	breast:
2	chr19:21950144..21952867-chr19:22033592..22036117,2	MCF-7	breast:
3	chr19:21948493..21950510-chr19:22018479..22020127,2	MCF-7	breast:

Variant related genes	Relation type
ZNF100	TF binding region
ENSG00000198521	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10412066	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11085494	0.84[ASN][1000 genomes]
rs11670736	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs12972593	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35717293	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4319878	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4338909	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4381721	0.98[ASN][1000 genomes]
rs4522535	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56168029	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61037485	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6511286	0.81[CEU][hapmap]
rs7246400	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252798	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102320	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv833783	chr19:21821406-21991838	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1815274	chr19:21825750-21981855	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv911426	chr19:21892040-21973929	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv911427	chr19:21900898-21960407	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv578970	chr19:21906655-21973929	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv961193	chr19:21911308-21950500	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv3342879	chr19:21913482-21968857	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1059457	chr19:21940891-21999025	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv578971	chr19:21950337-22008229	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs6511291	ZNF100	cis	Muscle Skeletal	GTEx
rs6511291	ZNF100	cis	Esophagus Mucosa	GTEx
rs6511291	VN1R84P	cis	Stomach	GTEx
rs6511291	RP11-420K14.3	cis	Heart Left Ventricle	GTEx
rs6511291	VN1R84P	cis	Artery Tibial	GTEx
rs6511291	ZNF100	cis	lung	GTEx
rs6511291	ZNF100	cis	Thyroid	GTEx
rs6511291	ZNF100	Cis_1M	lymphoblastoid	RTeQTL
rs6511291	ZNF100	cis	Artery Aorta	GTEx
rs6511291	VN1R84P	cis	Adipose Subcutaneous	GTEx
rs6511291	VN1R84P	cis	Thyroid	GTEx
rs6511291	ZNF100	cis	Stomach	GTEx
rs6511291	RP11-420K14.3	cis	Esophagus Muscularis	GTEx
rs6511291	ZNF100	cis	Artery Tibial	GTEx
rs6511291	VN1R84P	cis	Esophagus Muscularis	GTEx
rs6511291	ZNF100	cis	Whole Blood	GTEx
rs6511291	VN1R84P	cis	Nerve Tibial	GTEx
rs6511291	ZNF100	cis	Skin Sun Exposed Lower leg	GTEx
rs6511291	VN1R84P	cis	Whole Blood	GTEx
rs6511291	RP11-420K14.3	cis	Thyroid	GTEx
rs6511291	ZNF100	cis	Heart Left Ventricle	GTEx
rs6511291	VN1R84P	cis	lung	GTEx
rs6511291	VN1R84P	cis	Esophagus Mucosa	GTEx
rs6511291	ZNF100	cis	Nerve Tibial	GTEx
rs6511291	VN1R84P	cis	Muscle Skeletal	GTEx
rs6511291	ZNF100	cis	Adipose Subcutaneous	GTEx
rs6511291	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs6511291	VN1R84P	cis	Skin Sun Exposed Lower leg	GTEx
rs6511291	RP11-420K14.3	cis	lung	GTEx
rs6511291	RP11-420K14.3	cis	Adipose Subcutaneous	GTEx
rs6511291	ZNF100	cis	Esophagus Muscularis	GTEx
rs6511291	RP11-420K14.3	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21948400-21950600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:21948600-21950600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:21948600-21950600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:21948600-21950600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:21948600-21950600	Active TSS	Fetal Kidney	kidney
6	chr19:21948600-21950800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:21948600-21950800	Active TSS	Right Atrium	heart
8	chr19:21948600-21951200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:21948800-21950800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr19:21948800-21950800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:21949000-21950600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:21949000-21950600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:21949000-21950600	Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:21949000-21950600	Active TSS	Brain Hippocampus Middle	brain
15	chr19:21949000-21950600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr19:21949000-21950600	Active TSS	HMEC	breast
17	chr19:21949000-21950600	Active TSS	HUVEC	blood vessel
18	chr19:21949000-21950800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:21949000-21950800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:21949000-21950800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr19:21949000-21950800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr19:21949000-21950800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:21949000-21950800	Active TSS	Fetal Brain Female	brain
24	chr19:21949000-21950800	Active TSS	Stomach Smooth Muscle	stomach
25	chr19:21949000-21950800	Active TSS	GM12878-XiMat	blood
26	chr19:21949200-21950600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr19:21949200-21950600	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr19:21949200-21950600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:21949200-21950600	Active TSS	Fetal Intestine Large	intestine
30	chr19:21949200-21950600	Active TSS	Fetal Stomach	stomach
31	chr19:21949200-21950600	Active TSS	NHDF-Ad	bronchial
32	chr19:21949200-21950600	Active TSS	NHEK	skin
33	chr19:21949200-21950600	Active TSS	Osteobl	bone
34	chr19:21949200-21950800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr19:21949200-21950800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:21949200-21950800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:21949200-21950800	Active TSS	Primary T cells from cord blood	blood
38	chr19:21949200-21950800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:21949200-21950800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:21949200-21950800	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr19:21949200-21950800	Active TSS	Thymus	Thymus
42	chr19:21949200-21950800	Active TSS	K562	blood
43	chr19:21949200-21950800	Active TSS	NH-A	brain
44	chr19:21949200-21950800	Active TSS	NHLF	lung
45	chr19:21949400-21950600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:21949400-21950600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:21949400-21950600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:21949400-21950600	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr19:21949400-21950600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:21949400-21950600	Active TSS	Aorta	Aorta

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