Variant report

Variant	rs73935005
Chromosome Location	chr19:44029327-44029328
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	STAT3	chr19:44029293-44029873	MCF10A-Er-Src	breast:	n/a	chr19:44029755-44029763
2	PAX5	chr19:44028932-44029730	GM12891	blood:	n/a	chr19:44029496-44029505
3	EP300	chr19:44029306-44029579	GM12878	blood:	n/a	n/a
4	PAX5	chr19:44028958-44029661	GM12878	blood:	n/a	chr19:44029496-44029505
5	POLR2A	chr19:44029286-44030632	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:44029312-44029978	GM12892	blood:	n/a	n/a
7	MTA3	chr19:44028967-44030042	GM12878	blood:	n/a	n/a
8	STAT1	chr19:44029316-44030035	Hela-S3	cervix:	n/a	chr19:44030018-44030030 chr19:44029755-44029763
9	SPI1	chr19:44029312-44030036	HL-60	blood:	n/a	n/a
10	PAX5	chr19:44028804-44029693	GM12878	blood:	n/a	chr19:44029496-44029505
11	SPI1	chr19:44029301-44029669	GM12891	blood:	n/a	n/a
12	BCLAF1	chr19:44029300-44030016	GM12878	blood:	n/a	n/a
13	RUNX3	chr19:44028964-44029916	GM12878	blood:	n/a	n/a
14	ATF2	chr19:44029012-44030045	GM12878	blood:	n/a	n/a
15	RUNX3	chr19:44028976-44029865	GM12878	blood:	n/a	n/a
16	NFIC	chr19:44028939-44029720	GM12878	blood:	n/a	n/a
17	PAX5	chr19:44029073-44029349	GM12892	blood:	n/a	n/a
18	ZNF384	chr19:44029132-44029763	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44028119..44031033-chr19:44098735..44101211,2	MCF-7	breast:
2	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:
3	chr19:44029247..44034379-chr19:44035166..44038879,9	MCF-7	breast:

Variant related genes	Relation type
ZNF575	TF binding region
ENSG00000167378	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000176472	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11083710	1.00[EUR][1000 genomes]
rs25496	1.00[AMR][1000 genomes]
rs3213242	1.00[AMR][1000 genomes]
rs3213254	1.00[AMR][1000 genomes]
rs3213274	1.00[AMR][1000 genomes]
rs3213309	1.00[AMR][1000 genomes]
rs3213380	1.00[AMR][1000 genomes]
rs55908340	1.00[EUR][1000 genomes]
rs56284822	1.00[EUR][1000 genomes]
rs56296628	1.00[EUR][1000 genomes]
rs59051447	1.00[EUR][1000 genomes]
rs61732260	1.00[EUR][1000 genomes]
rs73935006	1.00[EUR][1000 genomes]
rs73937413	1.00[EUR][1000 genomes]
rs73937427	1.00[EUR][1000 genomes]
rs73937428	1.00[EUR][1000 genomes]
rs9653099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers 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 target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised 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	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44009200-44029600	Weak transcription	Psoas Muscle	Psoas
2	chr19:44011200-44029400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr19:44013200-44029800	Weak transcription	Small Intestine	intestine
4	chr19:44013400-44029400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:44014400-44029400	Weak transcription	Dnd41	blood
6	chr19:44015400-44029400	Weak transcription	Brain Germinal Matrix	brain
7	chr19:44015400-44029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:44015600-44029400	Weak transcription	Brain Anterior Caudate	brain
9	chr19:44015600-44029600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:44015800-44029400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr19:44015800-44029400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:44015800-44029400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:44015800-44029400	Weak transcription	Brain Angular Gyrus	brain
14	chr19:44015800-44029400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:44015800-44029400	Weak transcription	Fetal Brain Female	brain
16	chr19:44015800-44029400	Weak transcription	Left Ventricle	heart
17	chr19:44015800-44029800	Weak transcription	Aorta	Aorta
18	chr19:44015800-44030000	Weak transcription	Ovary	ovary
19	chr19:44017600-44029400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:44023800-44029400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:44024000-44029400	Weak transcription	K562	blood
22	chr19:44024200-44029400	Weak transcription	Fetal Lung	lung
23	chr19:44027200-44029600	Enhancers	Placenta	Placenta
24	chr19:44027400-44029400	Weak transcription	HSMMtube	muscle
25	chr19:44027600-44029400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:44028200-44029600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr19:44028400-44029400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr19:44028400-44029400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:44028600-44029400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:44028600-44029400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:44028600-44029400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr19:44028600-44029400	Enhancers	Adipose Nuclei	Adipose
33	chr19:44028600-44029400	Enhancers	Brain Hippocampus Middle	brain
34	chr19:44028600-44029400	Enhancers	Colon Smooth Muscle	Colon
35	chr19:44028600-44029600	Enhancers	Primary B cells from cord blood	blood
36	chr19:44028600-44029600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:44028600-44030600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr19:44028600-44030800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr19:44028800-44029400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:44028800-44029400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr19:44028800-44029400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr19:44028800-44029400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr19:44028800-44029400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr19:44028800-44029400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:44028800-44029400	Enhancers	Esophagus	oesophagus
46	chr19:44028800-44029400	Enhancers	Fetal Kidney	kidney
47	chr19:44028800-44029400	Active TSS	Rectal Smooth Muscle	rectum
48	chr19:44028800-44029400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr19:44028800-44029400	Enhancers	HepG2	liver
50	chr19:44028800-44029600	Enhancers	Primary neutrophils fromperipheralblood	blood

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