Variant report

Variant	rs2435048
Chromosome Location	chr19:22019697-22019698
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	POLR2A	chr19:22018148-22019724	PANC-1	pancreas:	n/a	n/a
2	MXI1	chr19:22018336-22019859	SK-N-SH	brain:	n/a	n/a
3	REST	chr19:22018086-22019788	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:21948493..21950510-chr19:22018479..22020127,2	MCF-7	breast:

Variant related genes	Relation type
ZNF43	TF binding region
ENSG00000197020	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10409809	0.81[EUR][1000 genomes]
rs10410478	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10413659	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418840	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420548	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672034	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2435039	0.80[GIH][hapmap]
rs28480566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4075276	0.81[EUR][1000 genomes]
rs62112965	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv3395280	chr19:21968753-22202288	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv911428	chr19:21986292-22106951	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv911429	chr19:21986292-22110219	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv961194	chr19:21998424-22019912	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv911430	chr19:22008229-22106951	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1062497	chr19:22013911-22102714	Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv543949	chr19:22013911-22102714	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2435048	RP11-420K14.3	cis	lung	GTEx
rs2435048	ZNF100	cis	Nerve Tibial	GTEx
rs2435048	ZNF100	cis	cerebellum	SCAN
rs2435048	VN1R84P	cis	lung	GTEx
rs2435048	ISYNA1	cis	cerebellum	SCAN
rs2435048	ZNF100	cis	parietal	SCAN
rs2435048	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs2435048	ZNF100	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22019000-22020400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:22019000-22020600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:22019000-22021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:22019000-22021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:22019000-22021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:22019000-22022200	Weak transcription	Spleen	Spleen
7	chr19:22019000-22022400	Weak transcription	Lung	lung
8	chr19:22019000-22022600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:22019000-22022600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:22019000-22022800	Weak transcription	Gastric	stomach
11	chr19:22019000-22024800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:22019000-22027800	Weak transcription	Small Intestine	intestine
13	chr19:22019000-22034200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:22019200-22019800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:22019200-22019800	Enhancers	Primary B cells from cord blood	blood
16	chr19:22019200-22019800	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:22019200-22019800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:22019200-22019800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:22019200-22020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:22019200-22021600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:22019200-22021600	Weak transcription	HSMM	muscle
22	chr19:22019200-22021800	Weak transcription	Ovary	ovary
23	chr19:22019200-22022000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:22019200-22022200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:22019200-22022600	Weak transcription	Aorta	Aorta
26	chr19:22019200-22022800	Weak transcription	Esophagus	oesophagus
27	chr19:22019200-22023000	Weak transcription	NHEK	skin
28	chr19:22019200-22023600	Weak transcription	HSMMtube	muscle
29	chr19:22019200-22025600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:22019200-22034000	Weak transcription	Colonic Mucosa	Colon
31	chr19:22019200-22034400	Weak transcription	Stomach Mucosa	stomach
32	chr19:22019400-22019800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr19:22019400-22019800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr19:22019400-22019800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr19:22019400-22019800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:22019400-22019800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:22019400-22019800	Enhancers	Fetal Thymus	thymus
38	chr19:22019400-22019800	Enhancers	Thymus	Thymus
39	chr19:22019400-22020000	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr19:22019400-22020400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:22019400-22020600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr19:22019400-22021400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:22019400-22021600	Weak transcription	Brain Germinal Matrix	brain
44	chr19:22019400-22021800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:22019400-22021800	Weak transcription	HUVEC	blood vessel
46	chr19:22019400-22021800	Weak transcription	K562	blood
47	chr19:22019400-22022400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:22019400-22022400	Weak transcription	NH-A	brain
49	chr19:22019400-22023800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:22019400-22033600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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