Variant report

Variant	rs3213242
Chromosome Location	chr19:44080725-44080726
allele	C/G
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	HA-E2F1	chr19:44078872-44080741	MCF-7	breast:	n/a	chr19:44080527-44080534 chr19:44080527-44080534 chr19:44079684-44079693 chr19:44080527-44080534 chr19:44079716-44079725 chr19:44079848-44079857 chr19:44079800-44079811
2	RFX5	chr19:44079064-44081406	SK-N-SH	brain:	n/a	chr19:44079923-44079932 chr19:44079821-44079835 chr19:44079921-44079935 chr19:44079823-44079832 chr19:44079920-44079935 chr19:44079819-44079833 chr19:44079919-44079933 chr19:44079918-44079934
3	EP300	chr19:44079036-44080900	SK-N-SH	brain:	n/a	chr19:44079378-44079385 chr19:44080824-44080837
4	RFX5	chr19:44079029-44081054	IMR90	lung:	n/a	chr19:44079923-44079932 chr19:44079821-44079835 chr19:44079921-44079935 chr19:44079823-44079832 chr19:44079920-44079935 chr19:44079819-44079833 chr19:44079919-44079933 chr19:44079918-44079934
5	MXI1	chr19:44078749-44080859	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44078455..44080853-chr19:44098810..44102178,4	MCF-7	breast:
2	chr19:44036185..44038265-chr19:44078295..44081409,3	K562	blood:
3	chr19:44077678..44083171-chr19:44093489..44103015,14	K562	blood:
4	chr19:44077932..44081099-chr19:44141868..44144910,3	MCF-7	breast:
5	chr19:44078643..44081382-chr19:44098876..44100782,4	K562	blood:
6	chr19:44078955..44081902-chr19:44082644..44085623,4	MCF-7	breast:
7	chr19:44079594..44081331-chr19:44123672..44125242,2	MCF-7	breast:
8	chr19:44079733..44081896-chr19:44082367..44084669,4	K562	blood:
9	chr19:44077687..44082496-chr19:44098234..44103069,7	MCF-7	breast:
10	chr19:44077515..44081647-chr19:44122454..44125105,4	K562	blood:
11	chr19:43991164..43993354-chr19:44079151..44081521,2	K562	blood:
12	chr19:44078733..44081444-chr19:44094635..44097229,2	MCF-7	breast:
13	chr19:44079920..44081896-chr19:44082367..44084716,3	K562	blood:

Variant related genes	Relation type
PINLYP	TF binding region
XRCC1	TF binding region
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000131116	Chromatin interaction
ENSG00000268361	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000073050	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs25496	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213259	1.00[LWK][hapmap];0.92[MKK][hapmap]
rs3213274	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs3213309	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3213380	1.00[AMR][1000 genomes]
rs73935005	1.00[AMR][1000 genomes]
rs9653099	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079200-44081600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:44079400-44080800	Active TSS	Brain Cingulate Gyrus	brain
3	chr19:44079800-44084000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:44079800-44085400	Weak transcription	Gastric	stomach
5	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
6	chr19:44080000-44080800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:44080000-44080800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr19:44080000-44081000	Enhancers	HepG2	liver
9	chr19:44080000-44081400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:44080200-44080800	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr19:44080200-44081000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:44080200-44081000	Flanking Active TSS	Esophagus	oesophagus
13	chr19:44080200-44081400	Flanking Active TSS	NHEK	skin
14	chr19:44080200-44084000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:44080400-44080800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:44080400-44080800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr19:44080400-44080800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:44080400-44080800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:44080400-44080800	Enhancers	Fetal Thymus	thymus
20	chr19:44080400-44080800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr19:44080400-44080800	Enhancers	Thymus	Thymus
22	chr19:44080400-44081000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:44080400-44081000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr19:44080400-44081000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:44080400-44081000	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:44080400-44081000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr19:44080400-44081000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr19:44080400-44081000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:44080400-44081000	Enhancers	Fetal Heart	heart
30	chr19:44080400-44081000	Enhancers	Fetal Muscle Trunk	muscle
31	chr19:44080400-44081000	Enhancers	Fetal Muscle Leg	muscle
32	chr19:44080400-44081000	Enhancers	Fetal Stomach	stomach
33	chr19:44080400-44081000	Enhancers	Pancreas	Pancrea
34	chr19:44080400-44081000	Enhancers	Stomach Smooth Muscle	stomach
35	chr19:44080400-44081000	Enhancers	GM12878-XiMat	blood
36	chr19:44080400-44081400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr19:44080400-44081400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:44080400-44081400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:44080400-44081600	Enhancers	HMEC	breast
40	chr19:44080400-44082400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:44080400-44083800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:44080400-44084000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:44080400-44084000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:44080400-44084000	Weak transcription	Brain Angular Gyrus	brain
45	chr19:44080400-44084000	Weak transcription	Brain Anterior Caudate	brain
46	chr19:44080400-44084000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:44080400-44084000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr19:44080400-44084000	Weak transcription	NHLF	lung
49	chr19:44080400-44084200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:44080400-44084200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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