Variant report

Variant	rs11952342
Chromosome Location	chr19:35351351-35351352
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	chr19:35351291-35351475	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:35351173-35351566	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:35351278-35351489	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr19:35351282-35351507	H1-hESC	embryonic stem cell:	n/a	n/a
5	EGR1	chr19:35351343-35351484	K562	blood:	n/a	n/a
6	TAF1	chr19:35351277-35351490	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOXA2	chr19:35351204-35351911	A549	lung:	n/a	n/a
8	POLR2A	chr19:35351112-35351593	MCF-7	breast:	n/a	n/a
9	HEY1	chr19:35351317-35351484	K562	blood:	n/a	n/a
10	POLR2A	chr19:35351319-35351468	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:35351215-35351454	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000271109	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11948548	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11955252	0.91[AFR][1000 genomes]
rs11958575	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065593	chr19:35315985-35363078	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1059180	chr19:35315985-35373739	Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1062596	chr19:35315985-35378095	Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1057673	chr19:35343922-35542878	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv543992	chr19:35343922-35542878	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35346200-35352800	Weak transcription	Stomach Mucosa	stomach
2	chr19:35349200-35351400	Active TSS	Primary T cells from cord blood	blood
3	chr19:35350200-35351400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:35350200-35351400	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr19:35350200-35351400	Active TSS	K562	blood
6	chr19:35350200-35351600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:35350200-35351600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:35350200-35351600	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr19:35350200-35351600	Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr19:35350200-35351600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr19:35350200-35351600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:35350200-35351600	Active TSS	HMEC	breast
13	chr19:35350600-35351400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:35350600-35351600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:35350600-35351600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:35350600-35351600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:35350600-35351600	Active TSS	Primary T cells fromperipheralblood	blood
18	chr19:35350600-35351600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr19:35350600-35351600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:35350600-35351600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr19:35350600-35351600	Active TSS	Adipose Nuclei	Adipose
22	chr19:35350600-35351600	Active TSS	Duodenum Mucosa	Duodenum
23	chr19:35350600-35351600	Active TSS	Fetal Thymus	thymus
24	chr19:35350600-35351600	Active TSS	Thymus	Thymus
25	chr19:35350600-35351800	Active TSS	H1 Cell Line	embryonic stem cell
26	chr19:35350600-35351800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:35350600-35351800	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:35350800-35351400	Active TSS	Primary B cells from cord blood	blood
29	chr19:35350800-35351400	Active TSS	Fetal Brain Female	brain
30	chr19:35350800-35351400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr19:35350800-35351600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr19:35350800-35351600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:35350800-35351600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:35350800-35351600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:35350800-35351600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:35350800-35351600	Active TSS	Primary B cells from peripheral blood	blood
37	chr19:35350800-35351600	Active TSS	Primary hematopoietic stem cells	blood
38	chr19:35350800-35351600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:35350800-35351600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:35350800-35351600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:35350800-35351600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:35350800-35351600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:35350800-35351600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:35350800-35351600	Active TSS	Brain Germinal Matrix	brain
45	chr19:35350800-35351600	Active TSS	Fetal Intestine Large	intestine
46	chr19:35350800-35351600	Active TSS	Fetal Intestine Small	intestine
47	chr19:35350800-35351600	Active TSS	Fetal Kidney	kidney
48	chr19:35350800-35351600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr19:35350800-35351600	Active TSS	Fetal Stomach	stomach
50	chr19:35350800-35351600	Active TSS	Left Ventricle	heart

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