Variant report

Variant	rs1230353
Chromosome Location	chr19:20193957-20193958
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	GATA3	chr19:20193639-20194187	MCF-7	breast:	n/a	n/a
2	FOXA1	chr19:20193821-20194010	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000240673	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1097511	0.81[AFR][1000 genomes]
rs11668688	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1230351	0.83[AFR][1000 genomes]
rs1230352	0.83[AFR][1000 genomes]
rs1654300	0.81[AFR][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	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
2	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
3	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
4	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
5	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
6	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
7	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
10	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
13	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
15	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
19	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
20	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1230353	ZNF682	cis	Muscle Skeletal	GTEx
rs1230353	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs1230353	ZNF253	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20190200-20194000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:20190200-20196200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:20190400-20194800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:20190400-20211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:20190600-20194400	Enhancers	Placenta	Placenta
6	chr19:20190600-20195600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:20190800-20194800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr19:20190800-20198200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:20191000-20195400	ZNF genes & repeats	Fetal Intestine Small	intestine
10	chr19:20191000-20198600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:20191200-20198800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:20191400-20198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:20192000-20194000	Enhancers	Fetal Lung	lung
14	chr19:20192000-20210200	Weak transcription	Ovary	ovary
15	chr19:20192200-20194800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:20192600-20194200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:20192600-20194600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:20192800-20194000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:20192800-20194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:20192800-20194800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:20193200-20194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:20193200-20194800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:20193400-20195000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:20193400-20195800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:20193600-20194000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
26	chr19:20193600-20194200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:20193600-20194200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:20193600-20194800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:20193600-20195600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:20193800-20194000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
31	chr19:20193800-20194200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr19:20193800-20194200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:20193800-20194200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:20193800-20194400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr19:20193800-20194400	Enhancers	Fetal Intestine Large	intestine
36	chr19:20193800-20194800	Genic enhancers	H1 Cell Line	embryonic stem cell
37	chr19:20193800-20194800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr19:20193800-20194800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:20193800-20194800	ZNF genes & repeats	Liver	Liver
40	chr19:20193800-20195000	ZNF genes & repeats	Fetal Stomach	stomach

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