Variant report

Variant	rs66624169
Chromosome Location	chr19:19971852-19971853
allele	G/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	TAF7	chr19:19971457-19972195	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:19971500-19972353	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr19:19971800-19972210	H1-hESC	embryonic stem cell:	n/a	n/a
4	GTF2F1	chr19:19971757-19972320	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF7	chr19:19971513-19972289	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:19971482-19972245	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr19:19971851-19972230	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr19:19971347-19972232	H1-hESC	embryonic stem cell:	n/a	chr19:19971601-19971610 chr19:19971596-19971615
9	MAX	chr19:19971444-19972193	H1-hESC	embryonic stem cell:	n/a	chr19:19971601-19971610 chr19:19971596-19971615
10	SP1	chr19:19971852-19972317	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr19:19971485-19972235	H1-hESC	embryonic stem cell:	n/a	chr19:19971708-19971718
12	CHD1	chr19:19971545-19972273	H1-hESC	embryonic stem cell:	n/a	chr19:19972107-19972117
13	POLR2A	chr19:19971317-19972366	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr19:19971360-19972202	H1-hESC	embryonic stem cell:	n/a	chr19:19972015-19972025 chr19:19972016-19972024 chr19:19972017-19972024 chr19:19972016-19972024
15	TAF1	chr19:19971442-19972322	H1-hESC	embryonic stem cell:	n/a	n/a
16	ELF1	chr19:19971845-19972118	K562	blood:	n/a	n/a
17	YY1	chr19:19971571-19972282	H1-hESC	embryonic stem cell:	n/a	chr19:19971708-19971718
18	MYC	chr19:19971521-19972064	H1-hESC	embryonic stem cell:	n/a	chr19:19971601-19971610 chr19:19971596-19971615
19	POLR2A	chr19:19971730-19971894	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:19971570-19972040	GM12892	blood:	n/a	n/a
21	SIN3A	chr19:19971435-19972221	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr19:19971769-19971941	K562	blood:	n/a	n/a
23	ATF2	chr19:19971653-19972027	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUND	chr19:19971828-19972175	H1-hESC	embryonic stem cell:	n/a	chr19:19972058-19972067
25	E2F6	chr19:19971623-19972263	H1-hESC	embryonic stem cell:	n/a	chr19:19972015-19972025 chr19:19972016-19972024 chr19:19972017-19972024 chr19:19972016-19972024
26	POLR2A	chr19:19971313-19972449	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:19971382-19972323	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBP	chr19:19971524-19972347	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr19:19971750-19972238	H1-hESC	embryonic stem cell:	n/a	chr19:19972107-19972117
30	TAF1	chr19:19971290-19972331	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr19:19971393-19972164	H1-hESC	embryonic stem cell:	n/a	chr19:19971601-19971610 chr19:19971596-19971615
32	REST	chr19:19971775-19972289	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP1	chr19:19971697-19972287	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19971677..19974532-chr19:19975356..19978312,2	MCF-7	breast:
2	chr19:19970667..19974781-chr19:19975210..19979739,6	K562	blood:

Variant related genes	Relation type
ZNF253	TF binding region
ENSG00000256771	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10421280	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327878	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12610390	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469700	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469702	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304169	0.87[AFR][1000 genomes]
rs3926422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250258	0.86[AFR][1000 genomes]
rs7252427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7260247	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic 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	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs66624169	ZNF253	cis	Nerve Tibial	GTEx
rs66624169	ZNF682	cis	Muscle Skeletal	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19970600-19972200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr19:19970800-19972200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:19971000-19972000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:19971000-19972200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:19971000-19972200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:19971000-19972200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:19971000-19972400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:19971200-19972000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:19971200-19972200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19971400-19972000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:19971400-19972000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:19971400-19972000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
13	chr19:19971400-19972200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:19971400-19972200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
15	chr19:19971400-19972200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:19971400-19972200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:19971400-19972200	ZNF genes & repeats	Liver	Liver
18	chr19:19971400-19972200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
19	chr19:19971400-19972200	Active TSS	Brain Hippocampus Middle	brain
20	chr19:19971400-19972200	Active TSS	Duodenum Mucosa	Duodenum
21	chr19:19971400-19972200	Active TSS	Fetal Intestine Large	intestine
22	chr19:19971400-19972200	Active TSS	Fetal Intestine Small	intestine
23	chr19:19971400-19972200	Active TSS	Fetal Kidney	kidney
24	chr19:19971400-19972200	ZNF genes & repeats	Fetal Thymus	thymus
25	chr19:19971400-19972400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr19:19971600-19972000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:19971600-19972000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr19:19971600-19972000	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr19:19971600-19972000	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr19:19971600-19972000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:19971600-19972000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:19971600-19972000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:19971600-19972000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr19:19971600-19972000	Active TSS	Fetal Lung	lung
35	chr19:19971600-19972000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr19:19971600-19972000	Active TSS	Rectal Smooth Muscle	rectum
37	chr19:19971600-19972000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
38	chr19:19971600-19972000	ZNF genes & repeats	NHEK	skin
39	chr19:19971600-19972200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:19971600-19972200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr19:19971600-19972200	Active TSS	Primary T cells from cord blood	blood
42	chr19:19971600-19972200	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:19971600-19972200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:19971600-19972200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
45	chr19:19971600-19972200	Active TSS	Brain Anterior Caudate	brain
46	chr19:19971600-19972200	Active TSS	Colon Smooth Muscle	Colon
47	chr19:19971600-19972200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:19971600-19972200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr19:19971600-19972200	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr19:19971600-19972200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle

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